Birrell Stewart, 30, was recovered from the water about a mile off the coast of East Wemyss, Fife, after the 10ft fishing boat capsized in the Firth of Forth shortly before 5pm on Monday.
He was airlifted to Ninewells Hospital in Dundee, where he died a short time later.
Jason Buchan, 35, and David Stead, 47, both from East Wemyss, remain missing.
The hunt for two fishermen missing after their boat overturned at sea has now moved to a search and recovery operation, police said as they confirmed the identity of a third crew member who died in the "tragic incident".
Deacon Jacqueline Thomson, who is parish assistant at Buckhaven and Wemyss parish Church of Scotland, said: "The community is deeply shocked and saddened by this fishing tragedy, which started off as something that many people in this part of the Fife Coast enjoy doing as a recreational pastime.
"On behalf of the Church we would wish to convey that our thoughts and prayers are with the families as they await news of their loved ones."
Mrs Thomson said the Church will support and comfort the families of those involved in the fishing tragedy as best as it can.
"This tragedy will be included in the public prayers at both West Wemyss and Buckhaven churches on Sunday," she added.
"As this situation progresses we shall endeavour to serve the people in this parish as best as we can as everyone comes in their sadness to recognise the tragedy of this situation."
Chief Inspector Adrian Annandale, area commander for Levenmouth, said: "This is a tragic incident and our thoughts are with Birrell's friends and family at this time.
"We are continuing to search the coast for both Jason Buchan and David Stead and our co-ordinated search activity will continue in the forthcoming days.
"Sadly, given the time that has passed since the incident was reported, we have now moved to a search and recovery operation."
