The pair had left the pier at Teelin on a small boat on Saturday but had not returned overnight.
The bodies of the men, believed to be a father and son, was recovered from the waters off Malinbeg at Glencolmcille in Donegal this afternoon.
A second body of a man in his 40s was then spotted by the crew of the helicopter.
Post mortems on two men - believed to be Lithuanian nationals - are due to be carried out today.
A boat was recovered washed up on a rocky stretch of coastline.
A Malin Head Coast Guard spokesman said: "Gardai called us this morning at 11am".
"There's quite a lot of cliff area in that region", said John Draper, divisional controller with the Irish Coast Guard. He was discovered by a farmer whose land runs down to the coast.
A major search and rescue operation was launched and a second body and a boat were found a short time later.
It has also been reported that the men were rescued from the same area just four weeks ago.
"It's the most tragic thing we experience in our community". Suspicions were raised when they did not return home last night. "I'm not a seafarer but those that know the sea know there are various currents that converge in this area and the sea is very strong".