The aircraft was found in a remote location close to Trawsfynydd, near Porthmadog, Gwynedd, with the two people on board pronounced dead at the scene, North Wales Police said.
The force received reports shortly after 12:00 BST that a light aircraft travelling from an airfield in England had not arrived at Caernarfon Airport as scheduled.
Multi-agency air and ground searches were carried out until the aircraft was found.
A team of investigators have since been deployed by the Air Accidents Investigations Branch (AAIB).
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