Both people -- a man and a woman -- were dead, U-T San Diego reported.
The plane, a single-engine Piers Mooney, was reported missing at 6:15 p.m. Wednesday, the San Diego County Sheriff's Department said.
Sgt. Don Parker said deputies tracked the cellphone of of the man on the plane.
The plane was discovered shortly after midnight Thursday in the Volcan Mountain Wilderness Preserve near Julian, Calif.
The plane -- which was headed to Gillespie Field in El Cajon, north of the city, when it vanished -- was registered to a 55-year-old San Diego man. Authorities did not immediately release the name of the man or the woman, the newspaper said.
A friend told the newspaper the man was an airplane mechanic and a competent pilot.
National Weather Service forecasters said wind gusts of 64 mph had been recorded on Volcan Mountain Wednesday.
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