diff --git a/PRESUBMIT.py b/PRESUBMIT.py
index e287e7eb50..3f0a72c7f1 100755
--- a/PRESUBMIT.py
+++ b/PRESUBMIT.py
@@ -68,7 +68,8 @@ BLACKLIST_LINT_FILTERS = [
 # 4. (later) The deprecated APIs are removed.
 NATIVE_API_DIRS = (
   'api',  # All subdirectories of api/ are included as well.
-  'media',
+  'media/base',
+  'media/engine',
   'modules/audio_device/include',
   'pc',
 )
diff --git a/native-api.md b/native-api.md
index b0ebe2762f..6e6251f387 100644
--- a/native-api.md
+++ b/native-api.md
@@ -14,7 +14,8 @@ legacy API directories—but see the
 Legacy API directory                       | Including subdirectories?
 -------------------------------------------|--------------------------
 `common_audio/include`                     | No
-`media`                                    | No
+`media/base`                               | No
+`media/engine`                             | No
 `modules/audio_coding/include`             | No
 `modules/audio_device/include`             | No
 `modules/audio_processing/include`         | No