diff --git a/js/roi/ROIManager.js b/js/roi/ROIManager.js
index 0f9e97f45..86fc49f40 100644
--- a/js/roi/ROIManager.js
+++ b/js/roi/ROIManager.js
@@ -274,6 +274,10 @@ class ROIManager {
         return this.roiSets.find(roiSet => true === roiSet.isUserDefined)
     }
 
+    deleteUserDefinedROISet(){
+        this.roiSets = this.roiSets.filter(roiSet => roiSet.isUserDefined !== true);
+    }
+    
     initializeUserDefinedROISet() {
 
         const config =
diff --git a/js/roi/ROIMenu.js b/js/roi/ROIMenu.js
index 539053c9f..c13cbfea9 100644
--- a/js/roi/ROIMenu.js
+++ b/js/roi/ROIMenu.js
@@ -109,8 +109,14 @@ class ROIMenu {
                 '<hr/>',
                 {
                     label: 'Delete',
-                    click: () => {
+                    click: async () => {
                         roiSet.removeFeature(feature)
+                        const userDefinedFeatures = await roiSet.getAllFeatures()
+                        
+                        // Delete user defined ROI Set if it is empty
+                        if (Object.keys(userDefinedFeatures).length === 0) {
+                            roiManager.deleteUserDefinedROISet()
+                        }
                         roiManager.deleteRegionWithKey(regionElement.dataset.region, columnContainer)
                         roiManager.repaintTable()
                     }
diff --git a/js/roi/ROISet.js b/js/roi/ROISet.js
index e97bbd845..2880f5de5 100644
--- a/js/roi/ROISet.js
+++ b/js/roi/ROISet.js
@@ -184,6 +184,10 @@ class DynamicFeatureSource {
         if (this.featureMap[chr]) {
             const match = `${chr}-${start}-${end}`
             this.featureMap[chr] = this.featureMap[chr].filter(feature => match !== `${feature.chr}-${feature.start}-${feature.end}`)
+            // Check if featureMap for a specific chromosome is empty now and delete it if yes
+            if (this.featureMap[chr].length === 0) {
+                delete this.featureMap[chr];
+            }
         }
     }
 }