diff --git a/rmgpy/rmg/model.py b/rmgpy/rmg/model.py
index 81873620506..c4f50fc89ad 100644
--- a/rmgpy/rmg/model.py
+++ b/rmgpy/rmg/model.py
@@ -1535,12 +1535,13 @@ def addReactionLibraryToEdge(self, reactionLibrary):
 
         # Perform species constraints and forbidden species checks
         for spec in self.newSpeciesList:
-            if database.forbiddenStructures.isMoleculeForbidden(spec.molecule[0]):
-                if 'allowed' in rmg.speciesConstraints and 'reaction libraries' in rmg.speciesConstraints['allowed']:
-                    spec.explicitlyAllowed = True
-                    logging.warning("Species {0} from reaction library {1} is globally forbidden.  It will behave as an inert unless found in a seed mechanism or reaction library.".format(spec.label, reactionLibrary.label))
-                else:
-                    raise ForbiddenStructureException("Species {0} from reaction library {1} is globally forbidden. You may explicitly allow it, but it will remain inert unless found in a seed mechanism or reaction library.".format(spec.label, reactionLibrary.label))
+            if not reactionLibrary.autoGenerated:  # No need to check for forbidden species otherwise
+                if database.forbiddenStructures.isMoleculeForbidden(spec.molecule[0]):
+                    if 'allowed' in rmg.speciesConstraints and 'reaction libraries' in rmg.speciesConstraints['allowed']:
+                        spec.explicitlyAllowed = True
+                        logging.warning("Species {0} from reaction library {1} is globally forbidden.  It will behave as an inert unless found in a seed mechanism or reaction library.".format(spec.label, reactionLibrary.label))
+                    else:
+                        raise ForbiddenStructureException("Species {0} from reaction library {1} is globally forbidden. You may explicitly allow it, but it will remain inert unless found in a seed mechanism or reaction library.".format(spec.label, reactionLibrary.label))
             if failsSpeciesConstraints(spec):
                 if 'allowed' in rmg.speciesConstraints and 'reaction libraries' in rmg.speciesConstraints['allowed']:
                     rmg.speciesConstraints['explicitlyAllowedMolecules'].extend(spec.molecule)