The pilot ejected and parachuted safely into a North Charleston neighborhood at about 2 p.m. He was taken to a local hospital, where he was in stable condition, said Maj. Melanie Salinas. The pilot's name has not been released.
Based on the missing plane's location and trajectory, the search for the F-35 Lightning II jet was focused on Lake Moultrie and Lake Marion, said Senior Master Sgt. Heather Stanton at Joint Base Charleston. Both lakes are north of North Charleston.
A South Carolina Law Enforcement Division helicopter joined the search for the F-35 after some bad weather cleared in the area, Stanton said. Military officials appealed in online posts Sunday for any help from the public in locating the aircraft.
Officials are still investigating why the pilot ejected, authorities said.
The pilot of a second F-35 returned safely to Joint Base Charleston, Salinas said.
The planes and pilots were with the Marine Fighter Attack Training Squadron 501 based in Beaufort, not far from South Carolina's Atlantic coast.