Albion's promotion challenge suffered a setback with their first League defeat in 12 matches under Peter Taylor.
A frenzied encounter at the JJB Stadium was effectively settled inside the opening 20 minutes by two Andy Liddell goals, the second a penalty.
Liddell completed his hat-trick with 14 minutes left to the delight of the home fans in a hostile crowd of 6,203.
Nothing went right for the Seagulls as Wigan, below par in the current campaign following a hat-trick of play-offs appearances extended their undefeated surge up the Second Division to 11 games.
Albion, with Kerry Mayo and Gary Hart back from injuries, began brightly but it all went downhill for them once Liddell gave the Latics a ninth minute lead.
Straight from the kick-off Hart made progress down the right before cutting inside, but his tame left-foot shot was easy for Filan.
But Wigan responded to the Seagulls' surge by almost scoring with their first attack in the fifth minute.
Teale, signed from Scottish club Ayr for £275,000 at the same time as Filan, got away from Mayo down the right.
His cross to the near post was met by Liddell with a firm downward header which forced Royce into a breathtaking deflection at the expense of a corner.
The reprieve for Albion did not last long as Wigan went ahead four minutes later.
McCulloch fed Liddell with space in which to manoeuvre. The ex-Barnsley man cut inside Cullip to fire a low right-foot drive past Royce from ten yards, his seventh of the season.
The key to under-achieving Wigan's extraordinary 6-1 home win against table-topping Stoke was an early lead and the Latics' tails were up following Liddell's strike.
Dinning, another big money buy from Wolves, fired straight at Royce from long range.
At the other end Jackson fell to the ground clutching his ankle with nobody near him.
The unfortunate Jackson had to be stretchered off, with Green taking his place at right back.
Albion's deficit doubled on 19 minutes with a penalty which prompted vehement protests by several Albion players.
Cullip was judged to have dragged down McCulloch from a ball over the top by Teale.
Referee Walton pointed straight to the spot and both Oatway and Watson made their feelings known to the Northants official, while Cullip complained to the linesman.
Once the dust had settled Liddell sent Royce the wrong way from the spot.
De Vos was booked for bringing down Hart on the brink of the Wigan box - although a number of Albion players felt the offence had occurred inside and they should have been awarded a penalty.
McMillan was cautioned for fouling Watson and the unrelenting incident continued with Liddell getting away from Morgan on the right wing as the Albion defender tried to tug him back.
Soon Morgan joined the yellow card contingent, apparently for his previous pulling at Liddell.
It was a costly fifth caution of the campaign for the former Fulham stalwart and a consequential automatic one-match ban.
Hart followed suit moments later for a foul on McMillan close to halfway.
Both Morgan and Hart will now be suspended from either a potential F.A. Cup game on January 26 or the home League match against Cardiff five days later.
Referee Walton handed out a fifth booking in the space of ten minutes when he cautioned Kennedy six minutes from the break for a tackle on Carpenter a few yards inside Wigan territory.
The Wigan fans were taunting Zamora, who was the subject of a rejected £1.5 million bid from the Lancashire club last season.
They felt a couple of challenges by Albion's prolific spearhead were worthy of him joining the caution count.
Liddell certainly ought to have had his name taken approaching the interval for an untidy challenge on Hart, who received some rough treatment throughout the half.
It had been a remarkable opening 45 minutes. Sadly for the Seagulls very little had gone right for them.
Royce re-emerged in a grey jersey after Wigan manager Paul Jewell complained during the half time interval that his red top had been indistinguishable from the Seagulls' red and black away kit.
Royce was soon in the wars again. He fell heavily over McCulloch in catching a high cross by Liddell and required lengthy treatment.
Albion, desperate for a goal to change the complexion of the contest, brought on Brooker for the battered Hart just beyond the hour mark.
They made another substitution on 67 minutes, youngster Virgo replacing Morgan at the heart of the defence.
Taylor made a final throw of the dice with 17 minutes remaining by introducing Webb upfront for his second appearance in place of defender Mayo.
But there was yet more anguish for Albion as Liddell completed his hat-trick on 81 minutes.
Albion were caught pushing up as Carpenter lost possession and Liddell raced clear to slot past the exposed Royce.
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