diff --git a/augur/utils.py b/augur/utils.py
index aff3033f7..35fe2ea7f 100644
--- a/augur/utils.py
+++ b/augur/utils.py
@@ -362,7 +362,7 @@ def _flatten(feature):
         feature_name = _lookup_feature_name_like_nextclade(feature)
         if feature_name == 'nuc':
             raise AugurError(f"Reference {reference!r} contains a gene with the name 'nuc'. This is not allowed.")
-        if feature_name in feature_names or feature_names is None:
+        if feature_names is None or feature_name in feature_names:
             features[feature_name] = feature
     
     if feature_names is not None: