Johan Elmander made the breakthrough and second-half goals from Kevin Davies (penalty), Fabrice Muamba and substitute Matt Taylor secured an emphatic victory.
Given they had beaten Liverpool only last Monday, Wigan manager Roberto Martinez would have expected much more from his side.
Instead they were off the pace and it was a day to forget for former Celtic defender Gary Caldwell.
Bolton made the breakthrough in the 10th minute after Davies managed to get the better of Titus Bramble.
The ball broke to Elmander and the Sweden striker shrugged off Caldwell to send a shot beyond Chris Kirkland for his third league goal of the campaign.
Elmander has been widely criticised for his lack of goals - his last one in the league came three months ago.
Wigan responded in the 19th minute and Paul Scharner got clear of his marker when Victor Moses, making his first start, floated in a free-kick.
However Scharner was unable to get enough power on his header and Jussi Jaaskelainen was able to make the save.
Play switched back down the other end and Davies latched on to a loose ball in the 24th minute only to send his effort high over the bar.
There was another scare for Wigan in the 26th minute when Lee Chung-yong delivered a corner from the left.
Davies was the first to react and eventually the ball broke to Andy O'Brien but his effort was diverted to safety.
Wigan launched a swift counter attack in the 36th minute and Charles N'Zogbia showed good pace to create an opening for himself.
However his effort from the edge of the area failed to trouble Jaaskelainen, much to the midfielder's frustration.
Wigan came close to equalising in the 43rd minute with N'Zogbia finding himself unmarked at the back post.
He clipped in a shot but Jaaskelainen was equal to it and parried the ball around the post.
Bolton extended their lead three minutes into the second half after Cohen was bundled over by Caldwell.
Referee Mike Dean had no hesitation in awarding a penalty despite Wigan's protests.
Davies stepped up and drilled his spot-kick into the corner for his seventh goal of the campaign.
It was just the start Bolton wanted and they made it 3-0 in the 53rd minute following some good skill from Muamba.
The 21-year-old midfielder is known for breaking up the play but he showed another side to his game by turning Caldwell inside out before firing a shot beyond Kirkland.
It was Muamba's first goal for the club since he arrived from Birmingham in the summer of 2008 and he marked the occasion by running to the dugout to embrace Coyle.
Wigan were stunned but Emmerson Boyce delivered a good cross into the area after 60 minutes, only for Rodallega to head over the bar.
Bolton went further clear in the 69th minute when Caldwell failed to deal with Elmander's back header and Taylor took advantage to score.
Ivan Klasnic almost added a fifth but his overhead kick in the 84th minute went the wrong side of the post following a flick on from Elmander.
Wigan kept working away and Bramble flicked a header wide but they still have work to do to avoid the drop.