diff --git a/git-difftool.perl b/git-difftool.perl
index 8cf0040590..ebd13baa6e 100755
--- a/git-difftool.perl
+++ b/git-difftool.perl
@@ -138,6 +138,7 @@ sub setup_dir_diff
 	my %submodule;
 	my %symlink;
 	my @working_tree = ();
+	my %working_tree_dups = ();
 	my @rawdiff = split('\0', $diffrtn);
 
 	my $i = 0;
@@ -188,6 +189,10 @@ EOF
 		}
 
 		if ($rmode ne $null_mode) {
+			# Avoid duplicate working_tree entries
+			if ($working_tree_dups{$dst_path}++) {
+				next;
+			}
 			my ($use, $wt_sha1) = use_wt_file($repo, $workdir,
 							  $dst_path, $rsha1);
 			if ($use) {
diff --git a/t/t7800-difftool.sh b/t/t7800-difftool.sh
index 4e713f7aa5..6a7207b950 100755
--- a/t/t7800-difftool.sh
+++ b/t/t7800-difftool.sh
@@ -419,6 +419,29 @@ run_dir_diff_test 'difftool --dir-diff when worktree file is missing' '
 	grep file2 output
 '
 
+run_dir_diff_test 'difftool --dir-diff with unmerged files' '
+	test_when_finished git reset --hard &&
+	test_config difftool.echo.cmd "echo ok" &&
+	git checkout -B conflict-a &&
+	git checkout -B conflict-b &&
+	git checkout conflict-a &&
+	echo a >>file &&
+	git add file &&
+	git commit -m conflict-a &&
+	git checkout conflict-b &&
+	echo b >>file &&
+	git add file &&
+	git commit -m conflict-b &&
+	git checkout master &&
+	git merge conflict-a &&
+	test_must_fail git merge conflict-b &&
+	cat >expect <<-EOF &&
+		ok
+	EOF
+	git difftool --dir-diff $symlinks -t echo >actual &&
+	test_cmp expect actual
+'
+
 write_script .git/CHECK_SYMLINKS <<\EOF
 for f in file file2 sub/sub
 do