The arrest of 23-year-old Dominique Demario Ellis comes a day after his alleged accomplice in the slaying, Marqueem Jermaine Mays, 25, was charged.
Richmond County Sheriff's Sgt. Calvin Chew said Ellis is charged with murder, possession of a firearm during the commission of a crime and aggravated assault.
A third man, Bennie Lorenzo Bell, 22, was arrested earlier this month.
Stokes, 37, was found dead on Dec. 28 at a boarding house in the 1600 block of Cleveland Street. He had been shot at least once.