ABC News reported that a spokesperson said one pilot ejected but it was "unclear whether the pilot was over land or water".
After the two were rescued, they were taken to a Florida hospital for treatment.
"I can confirm we have an F/A-18 down", Commander Dave Hecht told local media, confirming both pilots managed to eject.More news: 'Diddy', Curry among prospective Carolina Panthers owners
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Hecht did not describe the extent of their injuries.
Barbie Wilson, a local marina owner, witnessed the crash and called 911.
She said she didn't see the plane hit the water, but observed the crash site in shallow water offshore. I live in the neighborhood and so one was flying over.
"Literally, the wings went vertical, and there was a fireball, and it just literally dropped out of the sky", Wilson said. "It was like something out of a movie".