It is understood that Martinez was reluctant to coach in the Championship and felt he had given all he had to the club.
Confirming the news, Wigan chairman Dave Whelan said, per BBC Sport:
He feels he's not the man to lead us back into the Premier League. I've got to accept what he feels. He [Martinez] has 12 months left on his contract, so whoever comes in for him must pay the remainder of his contract.
The move is sure to grab the attention of Premier League clubs currently without managers with Everton, presently searching for a successor for David Moyes, being a likely destination.
Martinez has been linked with the Everton job ever since it became clear that David Moyes would not remain at the club and Dave Whelan reportedly told the media that Everton had inquired about Martinez, saying, "Everton rang me and I said they have permission to talk to him."
A former Wigan Athletic teammate of Martinez, Dutch defender Arjan de Zeeuw, recently claimed that Martinez would leave Wigan if there was Premier League interest in him. Speaking to the BBC, he said, "If there is interest from another Premier League club, I think Roberto will leave Wigan. [If I were Everton's chairman] I would definitely be asking the question and give him a phone call and see what his thoughts are."
Roberto Martinez has won two trophies so far in his managerial career: a Football League One trophy with Swansea City in 2007 and the 2013 FA Cup title with Wigan.