diff --git a/plugins/git4idea/src/git4idea/GitUtil.java b/plugins/git4idea/src/git4idea/GitUtil.java
index 9177f9d85312..19cc3bd36a1e 100644
--- a/plugins/git4idea/src/git4idea/GitUtil.java
+++ b/plugins/git4idea/src/git4idea/GitUtil.java
@@ -180,7 +180,8 @@ public class GitUtil {
     throws VcsException {
     Map<VirtualFile, List<VirtualFile>> result = new HashMap<VirtualFile, List<VirtualFile>>();
     for (VirtualFile file : virtualFiles) {
-      final VirtualFile vcsRoot = gitRootOrNull(file);
+      // directory is reported only when it is a submodule => it should be treated in the context of super-root
+      final VirtualFile vcsRoot = gitRootOrNull(file.isDirectory() ? file.getParent() : file);
       if (vcsRoot == null) {
         if (ignoreNonGit) {
           continue;