The man, identified only as being in his 50s, remained aboard the Carnival Elation after it docked Thursday morning in San Diego.
The man was detained by FBI agents after the 2,052-passenger Carnival Elation docked at its homeport in San Diego, FBI spokesman Darrell Foxworth said.
The identities of the couple were not immediately released.
The man and his 55-year-old wife got into a dispute in their cabin on Tuesday evening and she was killed, according to Foxworth and a statement from Carnival Cruise Lines.
Crew members found her body when they entered the cabin, Foxworth said. The man was taken into custody aboard the vessel put in the brig while it sailed home, Carnival said.
Security kept guard of the until the ship docked at 6:30 a.m. Thursday, said John Gilmore, a spokesman for the Port of San Diego.
The San Diego County medical examiner arrived and removed the woman's body about three hours later, he said.
Other passengers said they were told nothing official but rumors flew on the ship Wednesday that a man may have killed his wife.
Passenger Arlene Albi of San Diego said rumors started flying among passengers on Tuesday when they saw a security guard sitting outside the couple's cabin around the clock.
"I get up and go to the gym at 6 a.m. and he would be there," she said. "I'd look down the hall when I'd go back down, during the day, and he would still be sitting there. I don't know if it was the same guy, but there was always someone in front of that room."
Keith Slotter, the special agent in charge of the FBI's San Diego bureau, says 20 agents sailed out to the ship Wednesday night while it was at sea and questioned the man.
The Elation left San Diego on Saturday on a five-night cruise to Cabo San Lucas in Baja California.