He gave a start to Ishmel Demontagnac, whom Holloway has given a chance to revive his career after he was dismissed by Walsall because of indiscipline.
Demontagnac repaid Holloway's faith with a stunning third minute goal.
Ben Burgess got a vital touch and Demontagnac's pace took him past two markers before crashing home from 20 yards.
Wigan's early opportunities were a series of free kicks by Ben Watson but only one of the four forced Matt Gilks into a save.
Blackpool had a big penalty appeal turned down on seven minutes when Brett Ormerod was sandwiched in the box and Wigan had another let off when Antonio Amaya almost sliced an Ormerod cross into his own net.
On 19 minutes Blackpool went two ahead when Alhassan Bangura won a tackle in midfield. He fed Charlie Adam who delivered an inch-perfect pass to Burgess. Burgess appeared to only half hit his 18-yard shot but it carried enough power and direction to beat Mike Pollitt.
Some of the Wigan supporters made their way to the exits when the game was just 30 minutes old and Blackpool made it three.
Pollitt beat out a powerful effort from Demontagnac and the ball fell to Billy Clarke. He jinked into the box before he was unceremoniously hauled down by Amaya.
Adam took the penalty which Pollitt did brilliantly to save at full stretch but the skipper was alert enough to follow his effort up and tap in.
Roberto Martinez was clearly livid at his team's lack of determination apart from the distribution of Ben Watson and strong running of Scott Sinclair.
Blackpool saw off some Wigan pressure early in the second half to score again on 67 minutes when Adam, who dominated the midfield battle, sent a lovely ball through to sub Gary Taylor-Fletcher and he finished clinically from eight yards.
Ormerod had a late chance to make it five but was denied by Pollitt and Blackpool manager Holloway rubbed salt into the Wigan wounds when with eight minutes to go defender Alex John-Baptiste went off with a facial cut and Holloway decided to finish the game with ten men rather than replace him.
Wigan pulled one back in the third minute of injury time when Amaya powerfully headed home a corner.