The US Marine Corps on Thursday released a statement saying 2nd Lieutenant Ilario Pantano was charged on 1 February for his involvement in the shooting deaths of two Iraqi men in April last year during combat operations.
Pantano's civilian attorney, Charles Gittens, said the 33-year-old marine was charged with murder and "he has made it pretty firmly clear that he is not guilty".
The crime carries the death penalty but the Marine Corps has not said whether it will seek that punishment if he is convicted, Gittens said.
Pantano was the commander of a marine platoon sent to search a suspected hideout of armed fighters in an area south of Baghdad on 15 April.
The marines found weapons, ammunition and bomb-making material in the building and saw two men fleeing in a vehicle.
The marines shot at the vehicle's tyres to force it to a halt, took the two men into custody and ordered them to rip out the seats during a search for booby traps, Gittens said.
The lawyer said Pantano shot the two dead when he thought he was in danger.
Pantano served three more months in Iraq after the shooting and returned to Camp Lejeune when his tour of duty ended.