Police said formal identification of the body, which was discovered at Staffin Bay on Saturday, has yet to take place but relatives of Alasdair Macleod had been told.
A search was mounted after Mr Macleod, 57, from the Applecross area, was reported missing on November 20.
His empty boat Varuna was discovered with its engine running on rocks north of Applecross Bay, Wester Ross.
A Police Scotland spokeswoman said: “Inquiries remain ongoing. However, there are not thought to be any suspicious circumstances and a report will be submitted to the procurator fiscal in due course.”