Brian Thomson, who was 63, has been missing since the 16ft cruiser he was on with family members went down in Campbeltown Loch, Argyll and Bute, on August 19, 2007.
Police brought the wreckage of the boat ashore on Thursday, where the remains were found.
DNA test are to be carried out to formally identify them.
Mr Thomson's relatives have been informed of the development, although it may be weeks before the final results are known.
Another man and a 15-year-old boy were also on board the vessel, with witnesses reporting they had seen Mr Thomson go down with the boat.
The incident happened near Davaar Island, at the mouth of the sea loch.
The Herald's original report said one of the men phoned his wife to raise the alarm following the incident shortly after lunchtime.
She then alerted coastguards, and a lifeboat arrived about 20 minutes later.
The teenager and a 43-year-old man were recovered from the sea and taken to a local hospital but were not seriously injured, according to the report.
The initial search involved a Royal Navy helicopter from Prestwick, lifeboats, nearby vessels, the coastguard and police divers.
A Police Scotland spokeswoman said yesterday: "We can confirm that following a police search of Campbeltown Loch on Thursday July 10, human remains were recovered.
"These are being forensically examined to establish their identity."