Wigan suffered their third home loss in nine days on Sunday and following talks between Coyle and chairman Dave Whelan, the pair agreed to part company.
Coyle said: “It is with great sadness that we have made this decision and I would like to thank all my football staff and the staff at the club, who have been very supportive of me in my time here.
“I am confident that with this set of players, the team can keep moving in the right direction.”
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