Police and mountain rescue teams had launched a major search after the helicopter failed to arrive in Dublin on Wednesday afternoon after leaving the Luton area.
Superintendent Gareth Evans, of North Wales Police, said the details of the victims were not being released by police but specialist officers were supporting their families.
The privately-owned Twin Squirrel aircraft is believed to have left Milton Keynes to fly to Dublin, via Caernarfon Bay, before disappearing on Wednesday afternoon.
An extensive search of the Irish Sea and Snowdonia was launched at around 4.15pm on Wednesday after the Distress and Diversion system lost radar contact with the helicopter.
The search was scaled back overnight due to poor weather conditions but North Wales Police and mountain rescue teams continued the search on the ground.