There was no sign of 69-year-old Paul Clark, who sailed alone out of Prince Rupert, British Columbia, earlier in July on his way to Port Hardy, British Columbia.
A helicopter and Coast Guard vessels from Washington and Oregon searched for the Canadian for three hours without success.
The Coast Guard says a fishing vessel found his 16-foot sailboat. It's being transferred to Canadian officials.
Clark was last seen in the vicinity of Aristazabal Island, about half-way through his planned trip. He was reported missing after he failed to check in with his family.