An RAF search and rescue helicopter from RAF Valley and a mountain rescue team were dispatched to the scene.
A spokesman for RAF Valley said the details of the pilot's injuries are not yet known and would not speculate about the cause of the crash.
Dennis Morris, 68, who lives near the crash site, told the BBC News website he heard a noise "like a horrendous car crash with the screeching of metal". After looking out of his window he saw that the jet had broken in two in the crash.
RAF Valley trains fast jet combat pilots and is, according to its website, the "busiest station in the Royal Air Force".
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