John Angus Mowat, 33, went missing in July 1984 while fishing on the large lake, which is near the community of Burns Lake in B.C.'s Central Interior.
At the time, his boat was found with a fishing rod and freshly-caught fish in it, but his body was never recovered.
Last month, a survivor of the Burns Lake sawmill explosion was also presumed drowned while fishing on the lake, after a storm swamped his boat on June 7.
The family of Syd Neville, 35, hired a private search and recovery team, which located a body on the bottom of the lake using a sonar system.
Initially, it was assumed the body was Neville's, but after it was pulled from the lake on June 30, the B.C. Coroners Service determined that it was not. On Monday the B.C. Coroner confirmed the body was that of John Mowat.
Mowat's brother, Jim, says he was told on Friday that it was brother's remains that had been located 29 years after he first disappeared. He said the news came as a surprise after such a long time.
"No, it wasn't something we were expecting, even though it's always in the back of your mind when something happens on that lake. And our hearts go out the Nevilles for their loss, wish them a speedy closure."
Meanwhile, the community in Burns Lake is continuing to organize search efforts to locate Neville.
Previously, search efforts included bringing in the search team with special sonar equipment from Idaho, and using the services of a woman from Alberta who has a dog that can locate drowning victims through scent.
Francois Lake is 110 kilometres long and 245 metres deep, making it the second largest natural lake in B.C.