HM Coastguard helicopters had joined other search teams in the operation after the boat failed to return from a day trip as expected to Port Logan on Saturday evening.
The operation took place overnight and continued in areas the men may have travelled.
On Monday police named the men as Sandy Hamilton, 35, of Clydeview Cottages, Ashgill, Larkhall, and Kevin McKinlay, 46, of Rosslyn Road, also Larkhall.
Inspector Stephen Bell, Dumfries and Galloway Police Division, said: “Following a joint search operation by the Maritime and Coastguard Agency, the RNLI and Police Scotland, we can confirm that the bodies of two men have been recovered from the west coast of the Irish Sea.”
He added that enquiries were continuing into the incident and a report would be submitted to the Procurator Fiscal.
Among the coastguard teams from the south west involved were Ballantrae, Portpatrick, Stranraer and the Isle of Whithorn who were joined by colleagues from Northern Ireland.
Lifeboats were also launched from Port William and Stranraer as well as other crews from Northern Ireland and the Isle of Man.
Police Scotland state that they understand the men began their journey at Port Logan at around 9 am on Saturday.