diff --git a/docs/manifest-format.txt b/docs/manifest-format.txt
index c51b84be..9589352e 100644
--- a/docs/manifest-format.txt
+++ b/docs/manifest-format.txt
@@ -250,4 +250,6 @@ invocation, instructing repo to automatically download and manage
 these extra projects.
 
 Additional remotes and projects may also be added through a local
-manifest, stored in `$TOP_DIR/.repo/local_manifest.xml`.
+manifest, stored in `$TOP_DIR/.repo/local_manifest.xml`. This method
+is deprecated in favor of using multiple manifest files as mentioned
+above.
diff --git a/manifest_xml.py b/manifest_xml.py
index 4e476791..d16f1a98 100644
--- a/manifest_xml.py
+++ b/manifest_xml.py
@@ -300,6 +300,8 @@ class XmlManifest(object):
 
       local = os.path.join(self.repodir, LOCAL_MANIFEST_NAME)
       if os.path.exists(local):
+        print >>sys.stderr, 'warning: %s is deprecated; put local manifests in %s instead' % \
+                            (LOCAL_MANIFEST_NAME, LOCAL_MANIFESTS_DIR_NAME)
         nodes.append(self._ParseManifestXml(local, self.repodir))
 
       local_dir = os.path.abspath(os.path.join(self.repodir, LOCAL_MANIFESTS_DIR_NAME))