Tranmere's Johnstone's Paint Trophy campaign came to an end at the first hurdle with a 2-1 defeat against Fleetwood Town at Prenton Park.
Rovers led at half time through Evan Horwood's free kick but two goals from Jamille Matt turned the tie the way of the visitors in the second half.
Ronnie Moore made three changes to the side that started at Oldham with Akpo Sodje, Ryan Lowe and Andrai Jones replacing Jean-Louis Akpa Akpro, Jason Koumas and Danny Holmes.
Rovers started brightly and won a corner in the opening minute from which Ash Taylor rose highest at the back post to head over Chris Atkinson's right wing cross.
Lowe sent a 30 yard free kick inches wide of the left hand post on five minutes while Sodje had a shooting opportunity two minutes later after running on to Max Power's pass but the striker opted to pass and Fleetwood cleared the danger.
After Rovers cleared two tricky Fleetwood corners Stockton fired over at the opposite end while a cross from Lowe went straight through the six yard box and out the other side.
Ian Goodison blocked two crosses from the right wing on 14 minutes and two more a couple of minutes later as the visitors pressed and the veteran defender had to be at his best on 21 minutes to end a run from Jamille Matt, stretching out his leg as the striker ran towards goal to play the ball away and safely to Taylor.
Fleetwood broke quickly on 27 minutes after Taylor misjudged the flight of the ball but the visitors failed to take advantage of their numerical advantage in the attack as Matty Blair sliced wide from the edge of the area.
Gareth Evans forced Owain Fon Williams to save at his near post on 29 minutes from Matt's left wing cross while appeals for a free kick at the other end were turned down when Jones went down under a challenge from a defender when trying to run into the area to reach a one two pass from Sodje.
On 37 minutes Rovers took the lead. A foul on Sodje by Ryan Cresswell gave Rovers a free kick in a dangerous position just outside the area and Evan Horwood curled over the wall and into the right side of the net for his first goal for the Club.
However, two minutes into the second half the visitors equalised. Taylor and Fon Williams appeared to leave a long ball for each other allowing Jamille Matt to get between them and knock the ball into an empty net.
Sodje headed over from the third of three corners in quick succession on 54 minutes while Nathan Pond headed over Fon Williams' cross bar from close range from Junior Brown's cross.
Joe Thompson and Jake Kirby replaced James Rowe and Stockton on 64 minutes as Rovers switched from 4-3-1-2 to 4-4-2, but seconds later Fleetwood went ahead. Matt beat Goodison to a ball down the right wing and he flicked it over Taylor before running through on goal and sidefooting past Fon Williams into the bottom left corner.
Lowe's header was cleared off the line by Steven Schumacher on 69 minutes and the midfielder almost doubled Fleetwood's lead at the other end a couple of minutes later, hitting the side netting from a 20 yard free kick.
Matt got behind the Tranmere back four again on 78 minutes but could only hit the side netting from a tight angle and though Rovers looked for an opening late on they were unable to find a way past the Fleetwood defence.
Tranmere: Fon Williams, Jones, Taylor, Goodison, Horwood, Rowe (Thompson 64), Atkinson, Power, Lowe, Stockton (Kirby 64), Sodje (Akpa Akpro 80). Unused substitutes: Mooney, Holmes, Akpa Akpro.
Fleetwood: Davies, Howell, Murdoch, Pond, Evans, Schumacher, Matt (Ball 79 (Parkin 89), Brown, McLaughlin, Cresswell, Blair (Hughes 73). Unused substitutes: Roberts, Parkin, Lucas.
Referee: Carl Boyeson
Yellow cards: Schumacher (25), Pond (69)