Lieutenant Commander, Ian Molyneux, was shot dead on HMS Astute while it was docked in Southampton on 8th April.
Lieutenant Commander, Christopher Hodge, was also shot and remains in a serious but stable condition in hospital.
Able Seaman Ryan Samuel Donovan, who is 22, appeared at Southampton’s magistrates’ court and was then remanded in custody.
He will appear at Winchester Crown Court on Wednesday of this week.
Donovan has also been charged with the attempted murders of Petty Officer Christopher Brown, Chief Petty Officer David McCoy and Lieutenant Commander Hodge.