The Coast Guard's 5th District Command in Portsmouth said it spent the better part of Wednesday searching for the man after receiving a report at 4 a.m. that he was missing.
The sailing vessel In Tune sent out a mayday message after three boaters went overboard.
A tanker, the Stena Progress, responded to the call and rescued two of the yachters before the Coast Guard arrived.
The Coast Guard used a cutter and two helicopters launched from North Carolina and Massachusetts to search more than 1,000 nautical miles (3,430 square km) before calling off the search.
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