Chairman Phil Gartside said: “Owen poured his heart and soul into the job, both on and off the pitch, and he led our club with great dignity during some very challenging times.
“It is the right time for a change. We set a target at the beginning of the season and want to get back on track.
“I would like to place on record our sincere thanks to Owen, Sandy Stewart and Steve Davis for all their hard work during their time at Bolton Wanderers.”
Coyle said: “I have always been driven to act in the best interests of the club and care passionately about it.
“I had fantastic times here as a player and it has been a privilege to have held the post of manager.
“I want to thank the fans for their backing since I returned, the chairman Phil Gartside and the owner Eddie Davies for their support and friendship and the club’s staff and players for all their effort and commitment.
“I wish everyone connected with Bolton Wanderers all the very best.”
In the interim period, academy manager Jimmy Phillips and head of academy coaching and development Sammy Lee will take temporary charge of the first team squad.