Search and rescue teams were rushed to the area after the F/A-18 Hornet went down about 10:15 p.m. Wednesday.
The Hornet was flying with another plane which reported the crash.
The two Marines were rescued after about four hours in the water at about 2:30 a.m. Thursday and transported to Balboa Naval Medical Center in San Diego.
There was no word on what led to the crash. Officials said the missing jet was not recovered.
The Associated Press contributed to this report.