The pilot of the F-35B jet ejected and was being treated, while the crew of the KC-130J refueling aircraft had landed safely, the 3rd Marine Aircraft Wing said.
The crash occurred over Imperial County, California, ABC News reported.
"At approximately 1600 it was reported that an F-35B made contact with a KC-130J during an air-to-air refueling evolution, resulting in the crash of the F-35B," the 3rd Marine Aircraft Wing said in a tweet.
The cause of the crash was under investigation, the marines said.
The refueling plane had returned to Thermal Airport and all crew members were safe, it added.The marines unit did not immediately respond to a request for comment.