Authorities don't know how long the 27-foot boat, named "Casey Lynn," was floating off the coast. The boat's dingy is also still attached.
The U.S. Coast Guard has been searching the water for hours and still no sign of survivors.
After towing the vessel into the Marina Del Rey Harbor authorities were able to identify the boat's owner as Woodland Hills resident Michael Martinez.
Arson investigators said they would spend Tuesday night investigating the mystery.
It was possible the Martinez's car was found in the harbor parking lot.
Los Angeles Police were at Martinez's home in Woodland Hills speaking to his wife. Police said the couple is going through a divorce.
The Coast Guard is asking the public to call in with any additional information about the boat or its owner, U.S. Coast Guard (310) 521-3801.