The crash happened about 4 miles (6 kilometers) west of Marine Corps Air Station Beaufort.
The bad part came Friday morning, when another of the Marines' F-35 jets crashed during a training mission in SC, causing the pilot to safely eject.
"At approximately 11:45, a 2D Marine Aircraft Wing F-35B impacted near the Broad River in Beaufort County".
"The military has confirmed that it was a military plane".
A military official says the plane is a Marine F-35B fighter jet on a routine training mission. "More information will be provided as it becomes available".
"Our first priority will always be the safety of Marines, Sailors and the local community", Stephenson said.
"The US Marine pilot safely ejected from the single-seat aircraft and is now being evaluated by medical personnel", the Marines said in a statement.
"It's a total loss", an unnamed Marines official told the AFP news agency.
The F-35B is the only version of the aircraft that is able to land vertically like a helicopter. Few details were revealed about the airstrike.
The F-35 is the largest and most expensive weapons programme of its type in the world. The jet costs about $100 million.
"The F-35B is a significant enhancement in theater amphibious and air warfighting capability, operational flexibility and tactical supremacy", said Navy Vice Adm. Scott A. Stearney, commander of U.S. Naval Forces Central Command. The programme has been criticised for testing problems, delays and cost overruns.