The light aircraft, which had one pilot on board and no passengers, was last seen two miles northeast of Penmon in Anglesey, close to Puffin Island.
HM Coastguard said they received a call for assistance at around 12.47pm after the plane “disappeared from radar contact”.
The Air Accidents Investigation Branch said it had sent a team “to investigate an accident involving a light aircraft”.
According to the Flightradar website, a Cessna Skyhawk appears to have vanished from radar close to Puffin Island at 11.39am after descending from 1,900ft to 600ft. It had set off from Caernarfon Airport half an hour earlier.
North Wales Police said they were supporting the missing pilot’s family.
Chief Inspector Essi Ahari said: “North Wales Police are supporting HM Coastguard in a search for a light aircraft that was flying from Caernarfon Airport to the Great Orme in Llandudno and back this afternoon.
“The aircraft had one pilot on board and no other passengers and family liaison officers are supporting the missing pilot’s family”.
The RNLI said two lifeboats launched from Anglesey to assist in the search for the aircraft.
“The volunteer crews are searching an area around Penmon and are joined by Coastguard teams from Penmon and Bangor and a Coastguard helicopter,” a spokesperson added.
HM Coastguard said in a statement that it was co-ordinating the search and rescue operation in the Puffin Island area.
“The search and rescue helicopter from Caernarfon has been sent as well as Coastguard Rescue Teams from Penmon and Bangor and a Senior Coastguard Operations Officer”, the agency said.
“The RNLI lifeboats from Beaumaris, Moelfre and Llandudno and North Wales Police have been sent.”
The search operation was called off for the night at around 10pm and is due to resume on Tuesday morning.
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