diff --git a/src/flake8/main/setuptools_command.py b/src/flake8/main/setuptools_command.py
index ba5a260..a5d23a5 100644
--- a/src/flake8/main/setuptools_command.py
+++ b/src/flake8/main/setuptools_command.py
@@ -66,7 +66,7 @@ class Flake8(setuptools.Command):
             if package_directory.startswith(seen_package_directories):
                 continue
 
-            seen_package_directories += (package_directory,)
+            seen_package_directories += (package_directory + '.',)
             yield package_directory
 
     def module_files(self):
diff --git a/tests/unit/test_setuptools_command.py b/tests/unit/test_setuptools_command.py
new file mode 100644
index 0000000..40c9733
--- /dev/null
+++ b/tests/unit/test_setuptools_command.py
@@ -0,0 +1,34 @@
+"""Module containing tests for the setuptools command integration."""
+import pytest
+
+from setuptools import dist
+
+from flake8.main import setuptools_command
+
+
+@pytest.fixture
+def distribution():
+    """Create a setuptools Distribution object."""
+    return dist.Distribution({
+        'name': 'foo',
+        'packages': [
+            'foo',
+            'foo.bar',
+            'foo_biz',
+        ],
+    })
+
+
+@pytest.fixture
+def command(distribution):
+    """Create an instance of Flake8's setuptools command."""
+    return setuptools_command.Flake8(distribution)
+
+
+def test_package_files_removes_submodules(command):
+    """Verify that we collect all package files."""
+    package_files = list(command.package_files())
+    assert sorted(package_files) == [
+        'foo',
+        'foo_biz',
+    ]