The alarm was raised after the aircraft, which took off from Oban Airport at 11:30 on Thursday, failed to arrive at Carlisle Airport.
Police are investigating the circumstances surrounding the crash, which took place about two miles off the Kintyre coast near Skipness.
The bodies of two men and wreckage from the aircraft were recovered from the sea following an extensive search.
The search operation involved a coastguard search and rescue helicopter from Prestwick, as well as Police Scotland, Arran Lifeboat and the Tarbert and Campbeltown coastguard rescue teams.
Police Scotland said inquiries were continuing in an effort to establish the identities of the two men.
The force urged anyone with information about the crash to get in touch.
The Air Accidents Investigation Branch is also conducting an independent safety investigation.
Two men have been killed in a light aircraft crash off the Scottish coast.