Two men have died and one man has been rescued after their small fishing boat hit rocks and capsized in rough seas off Botany Bay on Sunday afternoon.

None of the fishermen were wearing lifejackets despite the "hazardous" conditions, said Westpac Life Saver Helicopter chief executive Stephen Leahy.

"Shortly after 1pm a small boat was hit by a wave and capsized at Cape Bailey south of Botany Bay," Mr Leahy said.

"Three people were thrown into the water and one managed to swim ashore. Two men have died. It appears that they have drowned," he said.

The two men were found floating face down in the water and were winched aboard the rescue helicopter where crews tried to resuscitate them, Mr Leahy said.