The agency had been searching for signs of Stuart Bee and his 32-foot boat since he was reported missing.
Bee left Port Canaveral on Friday, and was reported missing when he didn't return on Saturday.
A crew onboard the container ship Angeles spotted Bee some 86 miles off of Cape Canaveral on Sunday, the Coast Guard said in a Twitter post.
Courtesy: US Coast Guard/crew member aboard the m/v Angeles
Photos released by the Coast Guard showed Bee swimming from his sinking ship toward his rescuers and climbing aboard the container ship.
A Coast Guard helicopter crew flew to the Angeles to take Bee back to shore.
His condition wasn't immediately known.
The Associated Press contributed to this report.