diff --git a/clang/lib/Frontend/DependencyFile.cpp b/clang/lib/Frontend/DependencyFile.cpp
--- a/clang/lib/Frontend/DependencyFile.cpp
+++ b/clang/lib/Frontend/DependencyFile.cpp
@@ -108,7 +108,9 @@
 
 struct DepCollectorASTListener : public ASTReaderListener {
   DependencyCollector &DepCollector;
-  DepCollectorASTListener(DependencyCollector &L) : DepCollector(L) { }
+  FileManager &FileMgr;
+  DepCollectorASTListener(DependencyCollector &L, FileManager &FileMgr)
+      : DepCollector(L), FileMgr(FileMgr) {}
   bool needsInputFileVisitation() override { return true; }
   bool needsSystemInputFileVisitation() override {
     return DepCollector.needSystemDependencies();
@@ -124,6 +126,9 @@
     if (IsOverridden || IsExplicitModule)
       return true;
 
+    if (auto FE = FileMgr.getOptionalFileRef(Filename))
+      Filename = FE->getName();
+
     DepCollector.maybeAddDependency(Filename, /*FromModule*/true, IsSystem,
                                    /*IsModuleFile*/false, /*IsMissing*/false);
     return true;
@@ -176,7 +181,8 @@
       std::make_unique<DepCollectorMMCallbacks>(*this));
 }
 void DependencyCollector::attachToASTReader(ASTReader &R) {
-  R.addListener(std::make_unique<DepCollectorASTListener>(*this));
+  R.addListener(
+      std::make_unique<DepCollectorASTListener>(*this, R.getFileManager()));
 }
 
 DependencyFileGenerator::DependencyFileGenerator(
diff --git a/clang/lib/Frontend/ModuleDependencyCollector.cpp b/clang/lib/Frontend/ModuleDependencyCollector.cpp
--- a/clang/lib/Frontend/ModuleDependencyCollector.cpp
+++ b/clang/lib/Frontend/ModuleDependencyCollector.cpp
@@ -26,13 +26,17 @@
 /// Private implementations for ModuleDependencyCollector
 class ModuleDependencyListener : public ASTReaderListener {
   ModuleDependencyCollector &Collector;
+  FileManager &FileMgr;
 public:
-  ModuleDependencyListener(ModuleDependencyCollector &Collector)
-      : Collector(Collector) {}
+  ModuleDependencyListener(ModuleDependencyCollector &Collector,
+                           FileManager &FileMgr)
+      : Collector(Collector), FileMgr(FileMgr) {}
   bool needsInputFileVisitation() override { return true; }
   bool needsSystemInputFileVisitation() override { return true; }
   bool visitInputFile(StringRef Filename, bool IsSystem, bool IsOverridden,
                       bool IsExplicitModule) override {
+    if (auto FE = FileMgr.getOptionalFileRef(Filename))
+      Filename = FE->getName();
     Collector.addFile(Filename);
     return true;
   }
@@ -99,7 +103,8 @@
 }
 
 void ModuleDependencyCollector::attachToASTReader(ASTReader &R) {
-  R.addListener(std::make_unique<ModuleDependencyListener>(*this));
+  R.addListener(
+      std::make_unique<ModuleDependencyListener>(*this, R.getFileManager()));
 }
 
 void ModuleDependencyCollector::attachToPreprocessor(Preprocessor &PP) {
diff --git a/clang/test/Modules/dependency-gen-vfs.c b/clang/test/Modules/dependency-gen-vfs.c
new file mode 100644
--- /dev/null
+++ b/clang/test/Modules/dependency-gen-vfs.c
@@ -0,0 +1,32 @@
+// RUN: rm -rf %t
+// RUN: split-file %s %t
+
+//--- module.modulemap
+module M { header "m.h" }
+
+//--- m-real.h
+
+//--- overlay.json.template
+{
+  "version": 0,
+  "case-sensitive": "false",
+  "roots": [
+    {
+      "external-contents": "DIR/m-real.h",
+      "name": "DIR/m.h",
+      "type": "file"
+    }
+  ]
+}
+
+//--- tu.c
+#include "m.h"
+
+// RUN: sed -e "s|DIR|%/t|g" %t/overlay.json.template > %t/overlay.json
+// RUN: %clang_cc1 -fmodules -fimplicit-module-maps -fmodules-cache-path=%t/cache \
+// RUN:   -ivfsoverlay %t/overlay.json -dependency-file %t/tu.d -MT %t/tu.o -fsyntax-only %t/tu.c
+// RUN: cat %t/tu.d | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t
+// CHECK:      [[PREFIX]]/tu.o: \
+// CHECK-NEXT: [[PREFIX]]/tu.c \
+// CHECK-NEXT: [[PREFIX]]/module.modulemap \
+// CHECK-NEXT: [[PREFIX]]/m-real.h