Burnley met with Coyle last night in an attempt to persuade the manager who guided them to the Premier League to stay, but it seems they have been unsuccessful.
A Burnley statement read: "Owen Coyle has today reaffirmed his desire to leave Burnley Football Club and join Bolton Wanderers Football Club.
"Burnley Football Club will now enter discussions with Bolton Wanderers Football Club, due to the fact that compensation between the two parties has yet to be agreed.
"There will be no further comment at this time."
Burnley are thought to want around £3million in compensation for Coyle, who signed a 12-month extension to his existing three-year deal after being courted by Celtic in the summer.
Coyle, 43, was a popular figure as a player at Bolton in the mid-1990s.
Coyle, after previous spells in charge of Falkirk and St Johnstone, took over at Turf Moor in November 2007 having been recommended to the club, ironically, by Bolton.
Coyle had been considered by Bolton before Megson was appointed the previous month.
He quickly established a good reputation in England as his Burnley side impressed in cup competitions and then won promotion to the top flight - after a 33-year absence - via the play-offs.
Bolton are yet to comment.
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