Navy Capt. John Nettleton also has been charged with concealing material facts related to Christopher Tur's death. Tur's body was found floating in the water off the base in southeastern Cuba.
A federal indictment says Nettleton hid the fact that he was having an affair with Tur's wife and that the men had a fight the night of Tur's disappearance.
Nettleton was arrested Wednesday in Jacksonville, Florida.
A lawyer for Nettleton says he hasn't seen the indictment and is declining comment.
Nettleton commanded the Navy base but not the detention center where accused terrorists are held.
He was relieved of command in early 2015, amid a Naval Criminal Investigative Service investigation.