diff --git a/tests/commands/run_test.py b/tests/commands/run_test.py
index 6058df5d..d4e37f20 100644
--- a/tests/commands/run_test.py
+++ b/tests/commands/run_test.py
@@ -596,3 +596,26 @@ def test_unstaged_message_suppressed(
     args = _get_opts(**opts)
     ret, printed = _do_run(modified_config_repo, args)
     assert b'Your .pre-commit-config.yaml is unstaged.' not in printed
+
+
+def test_files_running_subdir(
+        repo_with_passing_hook, mock_out_store_directory, tempdir_factory,
+):
+    with cwd(repo_with_passing_hook):
+        install(Runner(repo_with_passing_hook))
+
+        os.mkdir('subdir')
+        open('subdir/foo.py', 'w').close()
+        cmd_output('git', 'add', 'subdir/foo.py')
+
+        with cwd('subdir'):
+            # Don't want to write to home directory
+            env = dict(os.environ, PRE_COMMIT_HOME=tempdir_factory.get())
+            # Use subprocess to demonstrate behaviour in main
+            _, stdout, _ = cmd_output(
+                sys.executable, '-m', 'pre_commit.main', 'run', '-v',
+                # Files relative to where we are (#339)
+                '--files', 'foo.py',
+                env=env,
+            )
+        assert 'subdir/foo.py' in stdout