A Coast Guard rescue swimmer plucked the two Marines from the ocean at about 2:30 a.m. and they were flown to a hospital where they were listed in stable condition, said Coast Guard Petty Officer 2nd Class Henry G. Dunphy.
"They were just basically floating in the water" when the crew of a search boat heard them calling for help about 35 miles offshore and called in a helicopter, Dunphy said.
The two were found about 85 miles southwest of San Diego, he said.
The Marines were aboard an F/A-18 Hornet that was flying with another jet that reported it missing around 10:15 p.m. Wednesday.
The other aircraft was able to tell the Coast Guard the general area where the plane vanished and an air and sea search began, Dunphy said.
The aircraft were based at the local Marine Corps Air Station Miramar.
The missing jet was not recovered, Dunphy said.