Other animals, including ferrets, were found during the raid in Huber Heights, the Dayton Daily News reported. But only the raccoon was illegal under Ohio law.
The man has not been identified or charged. The alligator was seized Sunday.
Wednesday's raid involved Huber Heights police officers, a state wildlife officer, the Ohio Department of Natural Resources and the Humane Society of Greater Dayton.
Officials say the alligator was small for its age, suggesting it was not being properly fed, and had broken and missing teeth. Videos posted on Facebook showed the alligator being mistreated with the owner and other people allegedly pouring alcohol on it and slamming it against a wall while making verbal taunts.