Capt. Wayne R. Brown, commanding officer of the San Diego-based amphibious assault ship, was relieved by Rear Adm. Frank L. Ponds, commander of Expeditionary Strike Group 3, said Lt. Rick Chernitzer, a spokesman for Naval Surface Force, U.S. Pacific Fleet.
The relief is not linked to a specific event, and the command investigation centered on Equal Opportunity concerns, Chernitzer said.
Brown took command of the Boxer on July 2, after a tour as executive officer of the ship. The Boxer returned in April from an eight-month deployment to the Pacific, the Horn of Africa and Central Command as part of the Boxer Amphibious Ready group and 13th Marine Expeditionary Unit.
Capt. Keith Moore, deputy commodore of Amphibious Squadron 1, has temporarily taken over Brown's duties, Chernitzer said.
Last week, Navy officials revealed that the executive officer of the San Diego-based USS Cowpens, who was relieved of his duties earlier this month, had driven away from the ship after testing above the legal driving limit for alcohol.
Cmdr. Armando Ramirez was found guilty of one count of drunken or reckless operation of a vehicle and one count of conduct unbecoming an officer at a hearing Sept. 17, officials said.