Two other civilians are also facing charges ranging from armed robbery to breaking and entering.
The three Marines are 20-year-old Kody Brittingham, 20-year-old Natalie Byrdsong and 22-year-old Curtis Groover, arcording to a Jacksonville newspaper.
Two others charged are 19-year-old Charles Anderson and 31-year-old Stanley Clyburn Jr.
Brittingham and Anderson are accused of entering the My Motel and shooting into a locked interior door before fleeing.
Authorities also believe Anderson was the gunman who took $1,472 from a Liberty Inn last month.
Police arrested four of the suspects after someone reported people breaking into vehicles at an apartment complex.