Three fishermen had been reported missing on Wednesday. The search was continuing, but high winds and rough water near the community of Balleoram slowed efforts.
There was no immediate word on the identity of the two bodies, but Steward May, the mayor of Belleoram, said they were found about eight kilometres from where the fishermen's boat capsized.
The seven-metre vessel, an uncovered fishing boat, as well as debris that included some fishing gear were recovered Thursday morning.
Friends of the trio have identified the missing fishermen as skipper Eric Savoury, 45, and teenage crew members A. J. Poole and Tim Cox.
A Hercules aircraft spotted the 7.5-metre boat in Fortune Bay Wednesday afternoon, a day after it was reported overdue. More debris was found Thursday morning.
At the time, Canadian Coast Guard research and rescue co-ordinator Christopher Fitzgerald said there was little hope of finding anyone alive.
Bill Fizzard
The ocean temperature in the area was about 8 C, he said, and even with the best survival gear, it's unlikely anyone submerged in water that cold would last more than 12 hours.
"I visited the families with the clergyman yesterday. It's difficult. It's really difficult for them," May said.
"It's taking a toll on them. I think we're a strong community, and we help each other. And I think what we mostly need is prayers and prayers and prayers."
The boat was found 30 metres offshore near the community of St. Jacques, dragging its anchor.
A search and rescue official told CBC News it could have capsized anywhere in Fortune Bay.
The search involved a French naval vessel from St. Pierre and Miquelon, Canadian Coast Guard boats and helicopters and RCMP officers who searched shorelines near where the boat was believed to have capsized.
Bill Fizzard, who has fished for lobster with Savoury, said earlier he didn't believe his friend would have tried to cross Fortune Bay to return home in bad weather.
"No, he shouldn't have been out there," he said of the boat's skipper, "but everyone is trying to make a living this time of year."
