Damian Zukaitis, 40, was taken into custody Saturday in San Bernardino County and faces charges of possession of a stolen airplane and taking stolen property across state lines, according to the county sheriff's department.
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Authorities say deputies also found a stash of beer and alcohol in the plane.
Air Force Search and Rescue notified the plane's owner after the aircraft's emergency location transmitter was activated. When the owner went to check on the plane, he saw it wasn't in the hangar.
The Federal Aviation Administration soon contacted the San Bernardino County Sheriff's Department and alerted them about the missing plane landing near Barstow-Daggett Airport.
Authorities say deputies responded to the scene and saw the suspect taxiing the aircraft on Minneola Road, heading back toward the airport.
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Zukaitis was arrested after he tried running away, according to the Sheriff's Department.
The aircraft was valued at about $80,000.
The Associated Press contributed to this report.