diff --git a/CHANGES.md b/CHANGES.md
index cf28c0831c..46a6856ecb 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -18,6 +18,7 @@
   that follows the semantic of the backend (js or wasm)
 * Compiler: warn on joo_global_object
 * Compiler: revisit static env handling (#1708)
+* Compiler: Emit index map when linking multiple js files together (#1714)
 * Runtime: change Sys.os_type on windows (Cygwin -> Win32)
 * Runtime: backtraces are really expensive, they need to be be explicitly
   requested at compile time (--enable with-js-error) or at startup (OCAMLRUNPARAM=b=1)
diff --git a/compiler/bin-js_of_ocaml/build_fs.ml b/compiler/bin-js_of_ocaml/build_fs.ml
index 3465edd4f9..5911760091 100644
--- a/compiler/bin-js_of_ocaml/build_fs.ml
+++ b/compiler/bin-js_of_ocaml/build_fs.ml
@@ -74,7 +74,7 @@ function jsoo_create_file_extern(name,content){
   let code = Code.prepend Code.empty instr in
   Filename.gen_file output_file (fun chan ->
       let pfs_fmt = Pretty_print.to_out_channel chan in
-      let (_ : Source_map.t option) =
+      let (_ : Source_map.Standard.t option) =
         Driver.f
           ~standalone:true
           ~wrap_with_fun:`Iife
diff --git a/compiler/bin-js_of_ocaml/cmd_arg.ml b/compiler/bin-js_of_ocaml/cmd_arg.ml
index fbaf4411ce..98d1cfee8a 100644
--- a/compiler/bin-js_of_ocaml/cmd_arg.ml
+++ b/compiler/bin-js_of_ocaml/cmd_arg.ml
@@ -43,7 +43,7 @@ type t =
   { common : Jsoo_cmdline.Arg.t
   ; (* compile option *)
     profile : Driver.profile option
-  ; source_map : (string option * Source_map.t) option
+  ; source_map : (string option * Source_map.Standard.t) option
   ; runtime_files : string list
   ; no_runtime : bool
   ; include_runtime : bool
@@ -302,13 +302,13 @@ let options =
       then
         let file, sm_output_file =
           match output_file with
-          | `Name file, _ when sourcemap_inline_in_js -> file, None
-          | `Name file, _ -> file, Some (chop_extension file ^ ".map")
-          | `Stdout, _ -> "STDIN", None
+          | `Name file, _ when sourcemap_inline_in_js -> Some file, None
+          | `Name file, _ -> Some file, Some (chop_extension file ^ ".map")
+          | `Stdout, _ -> None, None
         in
         Some
           ( sm_output_file
-          , { Source_map.version = 3
+          , { Source_map.Standard.version = 3
             ; file
             ; sourceroot = sourcemap_root
             ; sources = []
@@ -531,13 +531,13 @@ let options_runtime_only =
       then
         let file, sm_output_file =
           match output_file with
-          | `Name file, _ when sourcemap_inline_in_js -> file, None
-          | `Name file, _ -> file, Some (chop_extension file ^ ".map")
-          | `Stdout, _ -> "STDIN", None
+          | `Name file, _ when sourcemap_inline_in_js -> Some file, None
+          | `Name file, _ -> Some file, Some (chop_extension file ^ ".map")
+          | `Stdout, _ -> None, None
         in
         Some
           ( sm_output_file
-          , { Source_map.version = 3
+          , { Source_map.Standard.version = 3
             ; file
             ; sourceroot = sourcemap_root
             ; sources = []
diff --git a/compiler/bin-js_of_ocaml/cmd_arg.mli b/compiler/bin-js_of_ocaml/cmd_arg.mli
index c63aae2933..ec756685b5 100644
--- a/compiler/bin-js_of_ocaml/cmd_arg.mli
+++ b/compiler/bin-js_of_ocaml/cmd_arg.mli
@@ -23,7 +23,7 @@ type t =
   { common : Jsoo_cmdline.Arg.t
   ; (* compile option *)
     profile : Driver.profile option
-  ; source_map : (string option * Source_map.t) option
+  ; source_map : (string option * Source_map.Standard.t) option
   ; runtime_files : string list
   ; no_runtime : bool
   ; include_runtime : bool
diff --git a/compiler/bin-js_of_ocaml/compile.ml b/compiler/bin-js_of_ocaml/compile.ml
index cc7b2c34c6..2a71d0f24e 100644
--- a/compiler/bin-js_of_ocaml/compile.ml
+++ b/compiler/bin-js_of_ocaml/compile.ml
@@ -47,6 +47,7 @@ let output_gen ~standalone ~custom_header ~build_info ~source_map output_file f
     match source_map, sm with
     | None, _ | _, None -> ()
     | Some (output_file, _), Some sm ->
+        let sm = `Standard sm in
         let urlData =
           match output_file with
           | None ->
diff --git a/compiler/bin-js_of_ocaml/link.ml b/compiler/bin-js_of_ocaml/link.ml
index 0cd273b600..6b0f8add7f 100644
--- a/compiler/bin-js_of_ocaml/link.ml
+++ b/compiler/bin-js_of_ocaml/link.ml
@@ -23,7 +23,7 @@ open Cmdliner
 
 type t =
   { common : Jsoo_cmdline.Arg.t
-  ; source_map : (string option * Source_map.t) option
+  ; source_map : (string option * Source_map.Standard.t) option
   ; js_files : string list
   ; output_file : string option
   ; resolve_sourcemap_url : bool
@@ -96,13 +96,13 @@ let options =
       then
         let file, sm_output_file =
           match output_file with
-          | Some file when sourcemap_inline_in_js -> file, None
-          | Some file -> file, Some (chop_extension file ^ ".map")
-          | None -> "STDIN", None
+          | Some file when sourcemap_inline_in_js -> Some file, None
+          | Some file -> Some file, Some (chop_extension file ^ ".map")
+          | None -> None, None
         in
         Some
           ( sm_output_file
-          , { Source_map.version = 3
+          , { Source_map.Standard.version = 3
             ; file
             ; sourceroot = sourcemap_root
             ; sources = []
diff --git a/compiler/bin-jsoo_minify/jsoo_minify.ml b/compiler/bin-jsoo_minify/jsoo_minify.ml
index f607fa369b..b05145386f 100644
--- a/compiler/bin-jsoo_minify/jsoo_minify.ml
+++ b/compiler/bin-jsoo_minify/jsoo_minify.ml
@@ -92,7 +92,7 @@ let f { Cmd_arg.common; output_file; use_stdin; files } =
           if t () then (m ())#program p else p)
     in
     let p = Js_assign.program p in
-    let (_ : Source_map.t option) = Js_output.program pp p in
+    let (_ : Source_map.Standard.t option) = Js_output.program pp p in
     ()
   in
   with_output (fun out_channel ->
diff --git a/compiler/lib/driver.ml b/compiler/lib/driver.ml
index 4d2aa5ba90..6dbeb4f772 100644
--- a/compiler/lib/driver.ml
+++ b/compiler/lib/driver.ml
@@ -713,7 +713,7 @@ let full ~standalone ~wrap_with_fun ~profile ~link ~source_map ~formatter d p =
   emit formatter optimized_code
 
 let full_no_source_map ~formatter ~standalone ~wrap_with_fun ~profile ~link d p =
-  let (_ : Source_map.t option) =
+  let (_ : Source_map.Standard.t option) =
     full ~standalone ~wrap_with_fun ~profile ~link ~source_map:None ~formatter d p
   in
   ()
diff --git a/compiler/lib/driver.mli b/compiler/lib/driver.mli
index 91f846b989..5472edf5ae 100644
--- a/compiler/lib/driver.mli
+++ b/compiler/lib/driver.mli
@@ -35,11 +35,11 @@ val f :
   -> ?wrap_with_fun:[ `Iife | `Anonymous | `Named of string ]
   -> ?profile:profile
   -> link:[ `All | `All_from of string list | `Needed | `No ]
-  -> ?source_map:Source_map.t
+  -> ?source_map:Source_map.Standard.t
   -> formatter:Pretty_print.t
   -> Parse_bytecode.Debug.t
   -> Code.program
-  -> Source_map.t option
+  -> Source_map.Standard.t option
 
 val f' :
      ?standalone:bool
diff --git a/compiler/lib/js_assign.ml b/compiler/lib/js_assign.ml
index c12257d207..ca42b2ee9d 100644
--- a/compiler/lib/js_assign.ml
+++ b/compiler/lib/js_assign.ml
@@ -425,7 +425,7 @@ let program' (module Strategy : Strategy) p =
            "Some variables escaped (#%d). Use [--debug js_assign] for more info.@."
            (IdentSet.cardinal free)
        else
-         let (_ : Source_map.t option) =
+         let (_ : Source_map.Standard.t option) =
            Js_output.program
              ~accept_unnamed_var:true
              (Pretty_print.to_out_channel stderr)
diff --git a/compiler/lib/js_output.ml b/compiler/lib/js_output.ml
index 64dcdcab64..1c2fa741dc 100644
--- a/compiler/lib/js_output.ml
+++ b/compiler/lib/js_output.ml
@@ -1905,8 +1905,8 @@ let program ?(accept_unnamed_var = false) f ?source_map p =
   let names = Hashtbl.create 17 in
   let contents : Source_map.Source_content.t option list ref option =
     match source_map with
-    | None | Some { Source_map.sources_content = None; _ } -> None
-    | Some { Source_map.sources_content = Some _; _ } -> Some (ref [])
+    | None | Some { Source_map.Standard.sources_content = None; _ } -> None
+    | Some { Source_map.Standard.sources_content = Some _; _ } -> Some (ref [])
   in
   let push_mapping, get_file_index, get_name_index, source_map_enabled =
     let source_map_enabled =
@@ -1926,7 +1926,7 @@ let program ?(accept_unnamed_var = false) f ?source_map p =
                 loop xs ys
           in
           loop sm.sources (Option.value ~default:[] sm.sources_content);
-          List.iter sm.Source_map.names ~f:(fun f ->
+          List.iter sm.Source_map.Standard.names ~f:(fun f ->
               Hashtbl.add names f (Hashtbl.length names));
           true
     in
@@ -2014,7 +2014,7 @@ let program ?(accept_unnamed_var = false) f ?source_map p =
                     { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name })
         in
         let mappings = Source_map.Mappings.encode mappings in
-        Some { sm with Source_map.sources; names; sources_content; mappings }
+        Some { sm with Source_map.Standard.sources; names; sources_content; mappings }
   in
   PP.check f;
   (if stats ()
diff --git a/compiler/lib/js_output.mli b/compiler/lib/js_output.mli
index 5f8b95adb0..3b69d3de24 100644
--- a/compiler/lib/js_output.mli
+++ b/compiler/lib/js_output.mli
@@ -21,6 +21,6 @@
 val program :
      ?accept_unnamed_var:bool
   -> Pretty_print.t
-  -> ?source_map:Source_map.t
+  -> ?source_map:Source_map.Standard.t
   -> Javascript.program
-  -> Source_map.t option
+  -> Source_map.Standard.t option
diff --git a/compiler/lib/link_js.ml b/compiler/lib/link_js.ml
index e4d3d2989e..3c17bfedae 100644
--- a/compiler/lib/link_js.ml
+++ b/compiler/lib/link_js.ml
@@ -154,7 +154,7 @@ type action =
   | Drop
   | Unit
   | Build_info of Build_info.t
-  | Source_map of Source_map.t
+  | Source_map of Source_map.Standard.t
 
 let prefix_kind line =
   match String.is_prefix ~prefix:sourceMappingURL line with
@@ -170,6 +170,10 @@ let prefix_kind line =
       | true -> `Json_base64 (String.length sourceMappingURL_base64)
       | false -> `Url (String.length sourceMappingURL))
 
+let rule_out_index_map = function
+  | `Standard sm -> sm
+  | `Index _ -> failwith "unexpected index map at this stage"
+
 let action ~resolve_sourcemap_url ~drop_source_map file line =
   match prefix_kind line, drop_source_map with
   | `Other, (true | false) -> Keep
@@ -177,7 +181,8 @@ let action ~resolve_sourcemap_url ~drop_source_map file line =
   | `Build_info bi, _ -> Build_info bi
   | (`Json_base64 _ | `Url _), true -> Drop
   | `Json_base64 offset, false ->
-      Source_map (Source_map.of_string (Base64.decode_exn ~off:offset line))
+      Source_map
+        (rule_out_index_map (Source_map.of_string (Base64.decode_exn ~off:offset line)))
   | `Url _, false when not resolve_sourcemap_url -> Drop
   | `Url offset, false ->
       let url = String.sub line ~pos:offset ~len:(String.length line - offset) in
@@ -186,7 +191,7 @@ let action ~resolve_sourcemap_url ~drop_source_map file line =
       let l = in_channel_length ic in
       let content = really_input_string ic l in
       close_in ic;
-      Source_map (Source_map.of_string content)
+      Source_map (rule_out_index_map (Source_map.of_string content))
 
 module Units : sig
   val read : Line_reader.t -> Unit_info.t -> Unit_info.t
@@ -319,11 +324,12 @@ let link ~output ~linkall ~mklib ~toplevel ~files ~resolve_sourcemap_url ~source
       let sm_for_file = ref None in
       let ic = Line_reader.open_ file in
       let skip ic = Line_reader.drop ic in
+      let line_offset = Line_writer.lnum oc in
       let reloc = ref [] in
       let copy ic oc =
         let line = Line_reader.next ic in
         Line_writer.write ~source:ic oc line;
-        reloc := (Line_reader.lnum ic, Line_writer.lnum oc) :: !reloc
+        reloc := (Line_reader.lnum ic, Line_writer.lnum oc - line_offset) :: !reloc
       in
       let rec read () =
         match Line_reader.peek ic with
@@ -427,7 +433,7 @@ let link ~output ~linkall ~mklib ~toplevel ~files ~resolve_sourcemap_url ~source
           Line_writer.write_lines oc content);
       (match !sm_for_file with
       | None -> ()
-      | Some x -> sm := (x, !reloc) :: !sm);
+      | Some x -> sm := (x, !reloc, line_offset) :: !sm);
       match !build_info, build_info_for_file with
       | None, None -> ()
       | Some _, None -> ()
@@ -440,32 +446,32 @@ let link ~output ~linkall ~mklib ~toplevel ~files ~resolve_sourcemap_url ~source
   match source_map with
   | None -> ()
   | Some (file, init_sm) ->
-      let sm =
-        List.rev_map !sm ~f:(fun (sm, reloc) ->
+      let sections =
+        List.rev_map !sm ~f:(fun (sm, reloc, offset) ->
             let tbl = Hashtbl.create 17 in
             List.iter reloc ~f:(fun (a, b) -> Hashtbl.add tbl a b);
-            Source_map.filter_map sm ~f:(Hashtbl.find_opt tbl))
+            ( { Source_map.Index.gen_line = offset; gen_column = 0 }
+            , `Map (Source_map.Standard.filter_map sm ~f:(Hashtbl.find_opt tbl)) ))
       in
-      (match Source_map.merge (init_sm :: sm) with
-      | None -> ()
-      | Some sm -> (
-          (* preserve some info from [init_sm] *)
-          let sm =
-            { sm with
-              version = init_sm.version
-            ; file = init_sm.file
-            ; sourceroot = init_sm.sourceroot
-            }
-          in
-          match file with
-          | None ->
-              let data = Source_map.to_string sm in
-              let s = sourceMappingURL_base64 ^ Base64.encode_exn data in
-              Line_writer.write oc s
-          | Some file ->
-              Source_map.to_file sm file;
-              let s = sourceMappingURL ^ Filename.basename file in
-              Line_writer.write oc s));
+      let sm =
+        { Source_map.Index.version = init_sm.Source_map.Standard.version
+        ; file = init_sm.file
+        ; sections =
+            (* preserve some info from [init_sm] *)
+            List.map sections ~f:(fun (ofs, `Map sm) ->
+                ofs, `Map { sm with sourceroot = init_sm.sourceroot })
+        }
+      in
+      let sm = `Index sm in
+      (match file with
+      | None ->
+          let data = Source_map.to_string sm in
+          let s = sourceMappingURL_base64 ^ Base64.encode_exn data in
+          Line_writer.write oc s
+      | Some file ->
+          Source_map.to_file sm file;
+          let s = sourceMappingURL ^ Filename.basename file in
+          Line_writer.write oc s);
       if times () then Format.eprintf "  sourcemap: %a@." Timer.print t
 
 let link ~output ~linkall ~mklib ~toplevel ~files ~resolve_sourcemap_url ~source_map =
diff --git a/compiler/lib/link_js.mli b/compiler/lib/link_js.mli
index fbb70ef824..7e21a9fbbf 100644
--- a/compiler/lib/link_js.mli
+++ b/compiler/lib/link_js.mli
@@ -24,5 +24,5 @@ val link :
   -> toplevel:bool
   -> files:string list
   -> resolve_sourcemap_url:bool
-  -> source_map:(string option * Source_map.t) option
+  -> source_map:(string option * Source_map.Standard.t) option
   -> unit
diff --git a/compiler/lib/source_map.ml b/compiler/lib/source_map.ml
index a2d30d9f85..1ae1b2f099 100644
--- a/compiler/lib/source_map.ml
+++ b/compiler/lib/source_map.ml
@@ -210,151 +210,13 @@ module Mappings = struct
     readline 1 0 []
 end
 
-type t =
-  { version : int
-  ; file : string
-  ; sourceroot : string option
-  ; sources : string list
-  ; sources_content : Source_content.t option list option
-  ; names : string list
-  ; mappings : Mappings.t
-  }
-
-let empty ~filename =
-  { version = 3
-  ; file = filename
-  ; sourceroot = None
-  ; sources = []
-  ; sources_content = None
-  ; names = []
-  ; mappings = Mappings.empty
-  }
-
-let maps ~sources_offset ~names_offset x =
-  match x with
-  | Gen _ -> x
-  | Gen_Ori { gen_line; gen_col; ori_source; ori_line; ori_col } ->
-      let ori_source = ori_source + sources_offset in
-      Gen_Ori { gen_line; gen_col; ori_source; ori_line; ori_col }
-  | Gen_Ori_Name { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name } ->
-      let ori_source = ori_source + sources_offset in
-      let ori_name = ori_name + names_offset in
-      Gen_Ori_Name { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name }
-
-let filter_map sm ~f =
-  let a = Array.of_list (Mappings.decode sm.mappings) in
-  Array.stable_sort
-    ~cmp:(fun t1 t2 ->
-      match compare (gen_line t1) (gen_line t2) with
-      | 0 -> compare (gen_col t1) (gen_col t2)
-      | n -> n)
-    a;
-  let l = Array.to_list a |> List.group ~f:(fun a b -> gen_line a = gen_line b) in
-
-  let rec loop acc mapping =
-    match mapping with
-    | [] -> List.rev acc
-    | x :: xs ->
-        let gen_line = gen_line (List.hd x) in
-        let acc =
-          match f gen_line with
-          | None -> acc
-          | Some gen_line ->
-              List.rev_append_map
-                x
-                ~f:(function
-                  | Gen { gen_line = _; gen_col } -> Gen { gen_line; gen_col }
-                  | Gen_Ori { gen_line = _; gen_col; ori_source; ori_line; ori_col } ->
-                      Gen_Ori { gen_line; gen_col; ori_source; ori_line; ori_col }
-                  | Gen_Ori_Name
-                      { gen_line = _; gen_col; ori_source; ori_line; ori_col; ori_name }
-                    ->
-                      Gen_Ori_Name
-                        { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name })
-                acc
-        in
-        loop acc xs
-  in
-  let mappings = loop [] l in
-  { sm with mappings = Mappings.encode mappings }
-
-let merge = function
-  | [] -> None
-  | _ :: _ as l ->
-      let rec loop acc_rev mappings_rev ~sources_offset ~names_offset l =
-        match l with
-        | [] -> acc_rev, mappings_rev
-        | sm :: rest ->
-            let acc_rev, mappings_rev =
-              ( { acc_rev with
-                  sources = List.rev_append sm.sources acc_rev.sources
-                ; names = List.rev_append sm.names acc_rev.names
-                ; sources_content =
-                    (match sm.sources_content, acc_rev.sources_content with
-                    | Some x, Some acc_rev -> Some (List.rev_append x acc_rev)
-                    | None, _ | _, None -> None)
-                ; mappings = Mappings.empty
-                }
-              , List.rev_append_map
-                  ~f:(maps ~sources_offset ~names_offset)
-                  (Mappings.decode sm.mappings)
-                  mappings_rev )
-            in
-            loop
-              acc_rev
-              mappings_rev
-              ~sources_offset:(sources_offset + List.length sm.sources)
-              ~names_offset:(names_offset + List.length sm.names)
-              rest
-      in
-      let acc_rev, mappings_rev =
-        loop
-          { (empty ~filename:"") with sources_content = Some [] }
-          []
-          ~sources_offset:0
-          ~names_offset:0
-          l
-      in
-      Some
-        { acc_rev with
-          mappings = Mappings.encode (List.rev mappings_rev)
-        ; sources = List.rev acc_rev.sources
-        ; names = List.rev acc_rev.names
-        ; sources_content = Option.map ~f:List.rev acc_rev.sources_content
-        }
-
-(* IO *)
-
-let json t =
-  let rewrite_path path =
-    if Filename.is_relative path
-    then path
-    else
-      match Build_path_prefix_map.get_build_path_prefix_map () with
-      | Some map -> Build_path_prefix_map.rewrite map path
-      | None -> path
-  in
-  let stringlit s = `Stringlit (Yojson.Safe.to_string (`String s)) in
-  `Assoc
-    [ "version", `Intlit (string_of_int t.version)
-    ; "file", stringlit (rewrite_path t.file)
-    ; ( "sourceRoot"
-      , stringlit
-          (match t.sourceroot with
-          | None -> ""
-          | Some s -> rewrite_path s) )
-    ; "names", `List (List.map t.names ~f:(fun s -> stringlit s))
-    ; "sources", `List (List.map t.sources ~f:(fun s -> stringlit (rewrite_path s)))
-    ; "mappings", stringlit (Mappings.to_string t.mappings)
-    ; ( "sourcesContent"
-      , `List
-          (match t.sources_content with
-          | None -> []
-          | Some l ->
-              List.map l ~f:(function
-                  | None -> `Null
-                  | Some x -> Source_content.to_json x)) )
-    ]
+let rewrite_path path =
+  if Filename.is_relative path
+  then path
+  else
+    match Build_path_prefix_map.get_build_path_prefix_map () with
+    | Some map -> Build_path_prefix_map.rewrite map path
+    | None -> path
 
 let invalid () = invalid_arg "Source_map.of_json"
 
@@ -394,52 +256,324 @@ let list_stringlit_opt name rest =
     | _ -> invalid ()
   with Not_found -> None
 
-let of_json (json : Yojson.Raw.t) =
-  match json with
-  | `Assoc (("version", `Intlit version) :: rest) when int_of_string version = 3 ->
-      let string name json = Option.map ~f:string_of_stringlit (stringlit name json) in
-      let file =
-        match string "file" rest with
-        | None -> ""
-        | Some s -> s
-      in
-      let sourceroot = string "sourceRoot" rest in
-      let names =
-        match list_stringlit "names" rest with
-        | None -> []
-        | Some l -> List.map ~f:string_of_stringlit l
-      in
-      let sources =
-        match list_stringlit "sources" rest with
-        | None -> []
-        | Some l -> List.map ~f:string_of_stringlit l
-      in
-      let sources_content =
-        match list_stringlit_opt "sourcesContent" rest with
-        | None -> None
-        | Some l ->
-            Some
-              (List.map l ~f:(function
-                  | None -> None
-                  | Some s -> Some (Source_content.of_stringlit s)))
-      in
-      let mappings =
-        match string "mappings" rest with
-        | None -> Mappings.empty
-        | Some s -> Mappings.of_string s
-      in
-      { version = int_of_float (float_of_string version)
-      ; file
-      ; sourceroot
-      ; names
-      ; sources_content
-      ; sources
-      ; mappings
-      }
-  | _ -> invalid ()
+module Standard = struct
+  type t =
+    { version : int
+    ; file : string option
+    ; sourceroot : string option
+    ; sources : string list
+    ; sources_content : Source_content.t option list option
+    ; names : string list
+    ; mappings : Mappings.t
+    }
+
+  let empty =
+    { version = 3
+    ; file = None
+    ; sourceroot = None
+    ; sources = []
+    ; sources_content = None
+    ; names = []
+    ; mappings = Mappings.empty
+    }
+
+  let maps ~sources_offset ~names_offset x =
+    match x with
+    | Gen _ -> x
+    | Gen_Ori { gen_line; gen_col; ori_source; ori_line; ori_col } ->
+        let ori_source = ori_source + sources_offset in
+        Gen_Ori { gen_line; gen_col; ori_source; ori_line; ori_col }
+    | Gen_Ori_Name { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name } ->
+        let ori_source = ori_source + sources_offset in
+        let ori_name = ori_name + names_offset in
+        Gen_Ori_Name { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name }
+
+  let filter_map sm ~f =
+    let a = Array.of_list (Mappings.decode sm.mappings) in
+    Array.stable_sort
+      ~cmp:(fun t1 t2 ->
+        match compare (gen_line t1) (gen_line t2) with
+        | 0 -> compare (gen_col t1) (gen_col t2)
+        | n -> n)
+      a;
+    let l = Array.to_list a |> List.group ~f:(fun a b -> gen_line a = gen_line b) in
+
+    let rec loop acc mapping =
+      match mapping with
+      | [] -> List.rev acc
+      | x :: xs ->
+          let gen_line = gen_line (List.hd x) in
+          let acc =
+            match f gen_line with
+            | None -> acc
+            | Some gen_line ->
+                List.rev_append_map
+                  x
+                  ~f:(function
+                    | Gen { gen_line = _; gen_col } -> Gen { gen_line; gen_col }
+                    | Gen_Ori { gen_line = _; gen_col; ori_source; ori_line; ori_col } ->
+                        Gen_Ori { gen_line; gen_col; ori_source; ori_line; ori_col }
+                    | Gen_Ori_Name
+                        { gen_line = _; gen_col; ori_source; ori_line; ori_col; ori_name }
+                      ->
+                        Gen_Ori_Name
+                          { gen_line; gen_col; ori_source; ori_line; ori_col; ori_name })
+                  acc
+          in
+          loop acc xs
+    in
+    let mappings = loop [] l in
+    { sm with mappings = Mappings.encode mappings }
+
+  let merge = function
+    | [] -> None
+    | _ :: _ as l ->
+        let rec loop acc_rev mappings_rev ~sources_offset ~names_offset l =
+          match l with
+          | [] -> acc_rev, mappings_rev
+          | sm :: rest ->
+              let acc_rev, mappings_rev =
+                ( { acc_rev with
+                    sources = List.rev_append sm.sources acc_rev.sources
+                  ; names = List.rev_append sm.names acc_rev.names
+                  ; sources_content =
+                      (match sm.sources_content, acc_rev.sources_content with
+                      | Some x, Some acc_rev -> Some (List.rev_append x acc_rev)
+                      | None, _ | _, None -> None)
+                  ; mappings = Mappings.empty
+                  }
+                , List.rev_append_map
+                    ~f:(maps ~sources_offset ~names_offset)
+                    (Mappings.decode sm.mappings)
+                    mappings_rev )
+              in
+              loop
+                acc_rev
+                mappings_rev
+                ~sources_offset:(sources_offset + List.length sm.sources)
+                ~names_offset:(names_offset + List.length sm.names)
+                rest
+        in
+        let acc_rev, mappings_rev =
+          loop
+            { empty with sources_content = Some [] }
+            []
+            ~sources_offset:0
+            ~names_offset:0
+            l
+        in
+        Some
+          { acc_rev with
+            mappings = Mappings.encode (List.rev mappings_rev)
+          ; sources = List.rev acc_rev.sources
+          ; names = List.rev acc_rev.names
+          ; sources_content = Option.map ~f:List.rev acc_rev.sources_content
+          }
+
+  let json t =
+    let stringlit s = `Stringlit (Yojson.Safe.to_string (`String s)) in
+    `Assoc
+      (List.filter_map
+         ~f:(fun (name, v) ->
+           match v with
+           | None -> None
+           | Some v -> Some (name, v))
+         [ "version", Some (`Intlit (string_of_int t.version))
+         ; ( "file"
+           , match t.file with
+             | None -> None
+             | Some file -> Some (stringlit (rewrite_path file)) )
+         ; ( "sourceRoot"
+           , match t.sourceroot with
+             | None -> None
+             | Some s -> Some (stringlit (rewrite_path s)) )
+         ; "names", Some (`List (List.map t.names ~f:(fun s -> stringlit s)))
+         ; ( "sources"
+           , Some (`List (List.map t.sources ~f:(fun s -> stringlit (rewrite_path s)))) )
+         ; "mappings", Some (stringlit (Mappings.to_string t.mappings))
+         ; ( "sourcesContent"
+           , match t.sources_content with
+             | None -> None
+             | Some l ->
+                 Some
+                   (`List
+                     (List.map l ~f:(function
+                         | None -> `Null
+                         | Some x -> Source_content.to_json x))) )
+         ])
+
+  let of_json (json : Yojson.Raw.t) =
+    match json with
+    | `Assoc (("version", `Intlit version) :: rest) when int_of_string version = 3 ->
+        let string name json = Option.map ~f:string_of_stringlit (stringlit name json) in
+        let file = string "file" rest in
+        let sourceroot = string "sourceRoot" rest in
+        let names =
+          match list_stringlit "names" rest with
+          | None -> []
+          | Some l -> List.map ~f:string_of_stringlit l
+        in
+        let sources =
+          match list_stringlit "sources" rest with
+          | None -> []
+          | Some l -> List.map ~f:string_of_stringlit l
+        in
+        let sources_content =
+          match list_stringlit_opt "sourcesContent" rest with
+          | None -> None
+          | Some l ->
+              Some
+                (List.map l ~f:(function
+                    | None -> None
+                    | Some s -> Some (Source_content.of_stringlit s)))
+        in
+        let mappings =
+          match string "mappings" rest with
+          | None -> Mappings.empty
+          | Some s -> Mappings.of_string s
+        in
+        { version = int_of_float (float_of_string version)
+        ; file
+        ; sourceroot
+        ; names
+        ; sources_content
+        ; sources
+        ; mappings
+        }
+    | _ -> invalid ()
+
+  let to_string m = Yojson.Raw.to_string (json m)
+
+  let to_file m file = Yojson.Raw.to_file file (json m)
+end
+(* IO *)
+
+module Index = struct
+  type offset =
+    { gen_line : int
+    ; gen_column : int
+    }
+
+  type t =
+    { version : int
+    ; file : string option
+    ; sections : (offset * [ `Map of Standard.t ]) list
+    }
+
+  let json t =
+    let stringlit s = `Stringlit (Yojson.Safe.to_string (`String s)) in
+    `Assoc
+      (List.filter_map
+         ~f:(fun (name, v) ->
+           match v with
+           | None -> None
+           | Some v -> Some (name, v))
+         [ "version", Some (`Intlit (string_of_int t.version))
+         ; ( "file"
+           , match t.file with
+             | None -> None
+             | Some file -> Some (stringlit (rewrite_path file)) )
+         ; ( "sections"
+           , Some
+               (`List
+                 (List.map
+                    ~f:(fun ({ gen_line; gen_column }, `Map sm) ->
+                      `Assoc
+                        [ ( "offset"
+                          , `Assoc
+                              [ "line", `Intlit (string_of_int gen_line)
+                              ; "column", `Intlit (string_of_int gen_column)
+                              ] )
+                        ; "map", Standard.json sm
+                        ])
+                    t.sections)) )
+         ])
+
+  let intlit ~errmsg name json =
+    match List.assoc name json with
+    | `Intlit i -> int_of_string i
+    | _ -> invalid_arg errmsg
+    | exception Not_found -> invalid_arg errmsg
+
+  let section_of_json : Yojson.Raw.t -> offset * [ `Map of Standard.t ] = function
+    | `Assoc json ->
+        let offset =
+          match List.assoc "offset" json with
+          | `Assoc fields ->
+              let gen_line =
+                intlit
+                  "line"
+                  fields
+                  ~errmsg:
+                    "Source_map_io.Index.of_json: field 'line' absent or invalid from \
+                     section"
+              in
+              let gen_column =
+                intlit
+                  "column"
+                  fields
+                  ~errmsg:
+                    "Source_map_io.Index.of_json: field 'column' absent or invalid from \
+                     section"
+              in
+              { gen_line; gen_column }
+          | _ ->
+              invalid_arg "Source_map_io.Index.of_json: 'offset' field of unexpected type"
+        in
+        (match List.assoc "url" json with
+        | _ ->
+            invalid_arg
+              "Source_map_io.Index.of_json: URLs in index maps are not currently \
+               supported"
+        | exception Not_found -> ());
+        let map =
+          try Standard.of_json (List.assoc "map" json) with
+          | Not_found -> invalid_arg "Source_map_io.Index.of_json: field 'map' absent"
+          | Invalid_argument _ ->
+              invalid_arg "Source_map_io.Index.of_json: invalid sub-map object"
+        in
+        offset, `Map map
+    | _ -> invalid_arg "Source_map_io.Index.of_json: section of unexpected type"
+
+  let of_json = function
+    | `Assoc fields -> (
+        let string name json = Option.map ~f:string_of_stringlit (stringlit name json) in
+        let file = string "file" fields in
+        match List.assoc "sections" fields with
+        | `List sections ->
+            let sections = List.map ~f:section_of_json sections in
+            { version = 3; file; sections }
+        | _ -> invalid_arg "Source_map_io.Index.of_json: `sections` is not an array"
+        | exception Not_found ->
+            invalid_arg "Source_map_io.Index.of_json: no `sections` field")
+    | _ -> invalid_arg "Source_map_io.of_json: map is not an object"
+
+  let to_string m = Yojson.Raw.to_string (json m)
+
+  let to_file m file = Yojson.Raw.to_file file (json m)
+end
+
+type t =
+  [ `Standard of Standard.t
+  | `Index of Index.t
+  ]
+
+let of_json = function
+  | `Assoc fields as json -> (
+      match List.assoc "sections" fields with
+      | _ -> `Index (Index.of_json json)
+      | exception Not_found -> `Standard (Standard.of_json json))
+  | _ -> invalid_arg "Source_map_io.of_json: map is not an object"
 
 let of_string s = of_json (Yojson.Raw.from_string s)
 
-let to_string m = Yojson.Raw.to_string (json m)
+let of_file f = of_json (Yojson.Raw.from_file f)
 
-let to_file m file = Yojson.Raw.to_file file (json m)
+let to_string = function
+  | `Standard m -> Standard.to_string m
+  | `Index i -> Index.to_string i
+
+let to_file x f =
+  match x with
+  | `Standard m -> Standard.to_file m f
+  | `Index i -> Index.to_file i f
diff --git a/compiler/lib/source_map.mli b/compiler/lib/source_map.mli
index a5d6278329..c00e8872b9 100644
--- a/compiler/lib/source_map.mli
+++ b/compiler/lib/source_map.mli
@@ -67,27 +67,54 @@ module Mappings : sig
       function is mostly a no-op and is very cheap. *)
 end
 
-type t =
-  { version : int
-  ; file : string
-  ; sourceroot : string option
-  ; sources : string list
-  ; sources_content : Source_content.t option list option
-  ; names : string list
-  ; mappings : Mappings.t
-        (** Left uninterpreted, since most useful operations can be performed efficiently
+module Standard : sig
+  type t =
+    { version : int
+    ; file : string option
+    ; sourceroot : string option
+    ; sources : string list
+    ; sources_content : Source_content.t option list option
+    ; names : string list
+    ; mappings : Mappings.t
+          (** Left uninterpreted, since most useful operations can be performed efficiently
           directly on the encoded form, and a full decoding can be costly for big
           sourcemaps. *)
-  }
+    }
+
+  val filter_map : t -> f:(int -> int option) -> t
+  (** If [f l] returns [Some l'], map line [l] to [l'] (in the generated file) in
+    the returned debug mappings. If [f l] returns [None], remove debug mappings
+    which concern line [l] of the generated file. *)
 
-val filter_map : t -> f:(int -> int option) -> t
+  val merge : t list -> t option
+  (** Merge two lists of debug mappings. The time cost of the merge is more than
+    linear in function of the size of the input mappings. *)
+
+  val empty : t
+end
 
-val merge : t list -> t option
+module Index : sig
+  type offset =
+    { gen_line : int
+    ; gen_column : int
+    }
+
+  type nonrec t =
+    { version : int
+    ; file : string option
+    ; sections : (offset * [ `Map of Standard.t ]) list
+    }
+end
 
-val empty : filename:string -> t
+type t =
+  [ `Standard of Standard.t
+  | `Index of Index.t
+  ]
 
 val to_string : t -> string
 
 val to_file : t -> string -> unit
 
 val of_string : string -> t
+
+val of_file : string -> t
diff --git a/compiler/tests-compiler/build_path_prefix_map.ml b/compiler/tests-compiler/build_path_prefix_map.ml
index 6e2ce10fdc..29f9f7c8c3 100644
--- a/compiler/tests-compiler/build_path_prefix_map.ml
+++ b/compiler/tests-compiler/build_path_prefix_map.ml
@@ -20,6 +20,12 @@ open Js_of_ocaml_compiler.Stdlib
 open Util
 
 let%expect_test _ =
+  let print_section (sm : Js_of_ocaml_compiler.Source_map.Standard.t) =
+    Printf.printf "file: %s\n" (Option.value ~default:"<none>" sm.file);
+    Printf.printf "sourceRoot: %s\n" (Option.value ~default:"<none>" sm.sourceroot);
+    Printf.printf "sources:\n";
+    List.iter sm.sources ~f:(fun source -> Printf.printf "- %s\n" (normalize_path source))
+  in
   with_temp_dir ~f:(fun () ->
       let name = "test.ml" in
       Filetype.write_file name "let id x = x";
@@ -29,17 +35,14 @@ let%expect_test _ =
       |> compile_cmo_to_javascript ~sourcemap:true ~pretty:false
       |> extract_sourcemap
       |> function
-      | Some (sm : Js_of_ocaml_compiler.Source_map.t) ->
-          Printf.printf "file: %s\n" sm.file;
-          Printf.printf "sourceRoot: %s\n" (Option.value ~default:"<none>" sm.sourceroot);
-          Printf.printf "sources:\n";
-          List.iter sm.sources ~f:(fun source ->
-              Printf.printf "- %s\n" (normalize_path source))
+      | Some (`Standard (sm : Js_of_ocaml_compiler.Source_map.Standard.t)) ->
+          print_section sm
+      | Some (`Index i) -> List.iter i.sections ~f:(fun (_, `Map sm) -> print_section sm)
       | None -> failwith "no sourcemap generated!");
   [%expect
     {|
-      file: test.js
-      sourceRoot:
-      sources:
-      - /dune-root/test.ml
+    file: test.js
+    sourceRoot: <none>
+    sources:
+    - /dune-root/test.ml
     |}]
diff --git a/compiler/tests-compiler/macro.ml b/compiler/tests-compiler/macro.ml
index fe000c8e77..843583c4fa 100644
--- a/compiler/tests-compiler/macro.ml
+++ b/compiler/tests-compiler/macro.ml
@@ -31,7 +31,9 @@ let print_macro_transformed source =
       in
       let parsed = Util.parse_js source in
       let transformed, _ = Jsoo.Macro.f ~flags:false parsed in
-      let (_ : Jsoo.Source_map.t option) = Jsoo.Js_output.program pp transformed in
+      let (_ : Jsoo.Source_map.Standard.t option) =
+        Jsoo.Js_output.program pp transformed
+      in
       print_endline (Buffer.contents buffer))
 
 let print_macro_transformed source =
diff --git a/compiler/tests-compiler/sourcemap.ml b/compiler/tests-compiler/sourcemap.ml
index 6625996539..2aa2cdb9e1 100644
--- a/compiler/tests-compiler/sourcemap.ml
+++ b/compiler/tests-compiler/sourcemap.ml
@@ -20,7 +20,7 @@ open Js_of_ocaml_compiler
 open Stdlib
 open Util
 
-let print_mapping (sm : Source_map.t) =
+let print_mapping ~line_offset ~col_offset (sm : Source_map.Standard.t) =
   let sources = Array.of_list sm.sources in
   let _names = Array.of_list sm.names in
   let mappings = Source_map.Mappings.decode sm.mappings in
@@ -34,9 +34,10 @@ let print_mapping (sm : Source_map.t) =
             (file ori_source)
             ori_line
             ori_col
-            gen_line
-            gen_col
-      | Gen { gen_line; gen_col } -> Printf.printf "null -> %d:%d\n" gen_line gen_col)
+            (gen_line + line_offset)
+            (gen_col + col_offset)
+      | Gen { gen_line; gen_col } ->
+          Printf.printf "null -> %d:%d\n" (gen_line + line_offset) (gen_col + col_offset))
 
 let%expect_test _ =
   with_temp_dir ~f:(fun () ->
@@ -55,7 +56,14 @@ let%expect_test _ =
       print_file (Filetype.path_of_js_file js_file);
       match extract_sourcemap js_file with
       | None -> Printf.printf "No sourcemap found\n"
-      | Some sm -> print_mapping sm);
+      | Some (`Standard sm) -> print_mapping ~line_offset:0 ~col_offset:0 sm
+      | Some (`Index i) ->
+          List.iter
+            i.sections
+            ~f:(fun
+                ( ({ gen_line; gen_column } : Js_of_ocaml_compiler.Source_map.Index.offset)
+                , `Map sm )
+              -> print_mapping ~line_offset:gen_line ~col_offset:gen_column sm));
   [%expect
     {|
       $ cat "test.ml"
@@ -125,31 +133,35 @@ let%expect_test _ =
     Source_map.Gen_Ori
       { gen_line; gen_col; ori_source = source; ori_line = line; ori_col = col }
   in
-  let s1 : Source_map.t =
-    { (Source_map.empty ~filename:"1.map") with
+  let s1 : Source_map.Standard.t =
+    { Source_map.Standard.empty with
       names = [ "na"; "nb"; "nc" ]
     ; sources = [ "sa"; "sb" ]
     ; mappings =
         Source_map.Mappings.encode [ gen (1, 1) (10, 10) 0; gen (3, 3) (20, 20) 1 ]
     }
   in
-  let s2 : Source_map.t =
-    { (Source_map.empty ~filename:"2.map") with
+  let s2 : Source_map.Standard.t =
+    { Source_map.Standard.empty with
       names = [ "na2"; "nb2" ]
     ; sources = [ "sa2" ]
     ; mappings = Source_map.Mappings.encode [ gen (3, 3) (5, 5) 0 ]
     }
   in
-  let m = Source_map.merge [ s1; Source_map.filter_map s2 ~f:(fun x -> Some (x + 20)) ] in
+  let m =
+    Source_map.Standard.merge
+      [ s1; Source_map.Standard.filter_map s2 ~f:(fun x -> Some (x + 20)) ]
+  in
   (match m with
   | None -> ()
   | Some sm ->
-      let encoded_mappings = sm.Source_map.mappings in
+      let encoded_mappings = sm.Source_map.Standard.mappings in
       print_endline (Source_map.Mappings.to_string encoded_mappings);
-      print_mapping sm);
+      print_mapping ~line_offset:0 ~col_offset:0 sm);
   [%expect
     {|
     CASU;;GCUU;;;;;;;;;;;;;;;;;;;;GCff
     sa:10:10 -> 1:1
     sb:20:20 -> 3:3
-    sa2:5:5 -> 23:3 |}]
+    sa2:5:5 -> 23:3
+    |}]
diff --git a/compiler/tests-compiler/util/util.ml b/compiler/tests-compiler/util/util.ml
index 946b1472ec..965e3e0519 100644
--- a/compiler/tests-compiler/util/util.ml
+++ b/compiler/tests-compiler/util/util.ml
@@ -421,7 +421,7 @@ let program_to_string ?(compact = false) p =
   let buffer = Buffer.create 17 in
   let pp = Jsoo.Pretty_print.to_buffer buffer in
   Jsoo.Pretty_print.set_compact pp compact;
-  let (_ : Jsoo.Source_map.t option) = Jsoo.Js_output.program pp p in
+  let (_ : Jsoo.Source_map.Standard.t option) = Jsoo.Js_output.program pp p in
   (* This final comment should help to keep merge-confict inside
      {| .. |}, allowing to resolve confict with [dune promote]. *)
   Buffer.add_string buffer "//end\n";
diff --git a/compiler/tests-sourcemap/dump.reference b/compiler/tests-sourcemap/dump.reference
index d9a8cf150c..be88f6df65 100644
--- a/compiler/tests-sourcemap/dump.reference
+++ b/compiler/tests-sourcemap/dump.reference
@@ -1,7 +1,7 @@
 sourcemap for test.bc.js
-b.ml:1:4 -> 12:   function <>f(x){return x - 1 | 0;}
-b.ml:1:6 -> 14:   function f(<>x){return x - 1 | 0;}
-b.ml:1:10 -> 17:   function f(x){<>return x - 1 | 0;}
-b.ml:1:6 -> 24:   function f(x){return <>x - 1 | 0;}
-b.ml:1:15 -> 34:   function f(x){return x - 1 | 0;<>}
-b.ml:1:4 -> 23:   var Testlib_B = [0, <>f];
+/my/sourceRoot#b.ml:1:4 -> 12:   function <>f(x){return x - 1 | 0;}
+/my/sourceRoot#b.ml:1:6 -> 14:   function f(<>x){return x - 1 | 0;}
+/my/sourceRoot#b.ml:1:10 -> 17:   function f(x){<>return x - 1 | 0;}
+/my/sourceRoot#b.ml:1:6 -> 24:   function f(x){return <>x - 1 | 0;}
+/my/sourceRoot#b.ml:1:15 -> 34:   function f(x){return x - 1 | 0;<>}
+/my/sourceRoot#b.ml:1:4 -> 23:   var Testlib_B = [0, <>f];
diff --git a/compiler/tests-sourcemap/dump_sourcemap.ml b/compiler/tests-sourcemap/dump_sourcemap.ml
index 27dfa136f3..59bb828bd9 100644
--- a/compiler/tests-sourcemap/dump_sourcemap.ml
+++ b/compiler/tests-sourcemap/dump_sourcemap.ml
@@ -36,7 +36,7 @@ let extract_sourcemap lines =
       Some (Source_map.of_string content)
   | _ -> None
 
-let print_mapping lines (sm : Source_map.t) =
+let print_mapping lines ?(line_offset = 0) (sm : Source_map.Standard.t) =
   let lines = Array.of_list lines in
   let sources = Array.of_list sm.sources in
   let _names = Array.of_list sm.names in
@@ -62,15 +62,30 @@ let print_mapping lines (sm : Source_map.t) =
         -> (
           match file ori_source with
           | "a.ml" | "b.ml" | "c.ml" | "d.ml" ->
+              let root =
+                match sm.sourceroot with
+                | None -> ""
+                | Some root -> root ^ "#"
+              in
               Printf.printf
-                "%s:%d:%d -> %d:%s\n"
+                "%s%s:%d:%d -> %d:%s\n"
+                root
                 (file ori_source)
                 ori_line
                 ori_col
                 gen_col
-                (mark gen_col lines.(gen_line - 1))
+                (mark gen_col lines.(gen_line - 1 + line_offset))
           | _ -> ()))
 
+let print_sourcemap lines = function
+  | `Standard sm -> print_mapping lines sm
+  | `Index l ->
+      List.iter
+        l.Source_map.Index.sections
+        ~f:(fun (Source_map.Index.{ gen_line; gen_column }, `Map sm) ->
+          assert (gen_column = 0);
+          print_mapping lines ~line_offset:gen_line sm)
+
 let files = Sys.argv |> Array.to_list |> List.tl
 
 let () =
@@ -80,4 +95,4 @@ let () =
       | None -> Printf.printf "not sourcemap for %s\n" f
       | Some sm ->
           Printf.printf "sourcemap for %s\n" f;
-          print_mapping lines sm)
+          print_sourcemap lines sm)
diff --git a/compiler/tests-sourcemap/dune b/compiler/tests-sourcemap/dune
index e690f5a3ee..6c96b3aef1 100644
--- a/compiler/tests-sourcemap/dune
+++ b/compiler/tests-sourcemap/dune
@@ -7,6 +7,9 @@
  (name test)
  (modules test)
  (modes js)
+ (js_of_ocaml
+  (link_flags
+   (:standard --source-map-root /my/sourceRoot)))
  (libraries testlib))
 
 (library