The deceased man and woman, Americans thought to be around 50, were found Thursday morning in their cabin, Puerto Rican media said, citing police.
FBI spokesman Moises Quinones told AFP that the agency was handling the investigation but could not confirm any other details.
"At approximately 11:30 am local time, two guests onboard MS Ryndam were found deceased in their stateroom in what appears to be a murder-suicide," cruise line Holland America said yesterday.
"We are terribly saddened by this tragic event and our thoughts and prayers are with the families and friends of these guests at this difficult time."
The MS Ryndam, which can carry up to 1,260 passengers and 580 crew members, set sail on March 29 from Tampa, Florida in the United States, for a two-week tour of the Caribbean.