Assistant Coach Rob Zettler was reassigned within the organization.
Wilson had been with the Maple Leafs since the start of the 2008-09 season and leaves the team with a record of 130-135-45. Toronto has lost its last six games and is in fourth place in the Northeast Division, five points out of a playoff position.
"This was not an easy decision for me to make," General Manager Brian Burke said. "I want to thank Ron for all of his hard work and dedication to our organization over the past four seasons."
Carlyle, 55, was fired this season by Anaheim after the Ducks got off to a 7-13-4 start. He had been with that franchise for seven years.
Carlyle becomes the second NHL coach this season to be fired from one team and hired to lead another. Bruce Boudreau, who was dismissed by the Washington Capitals, replaced Carlyle in Anaheim.
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