The Shrimps slipped to a 1-0 defeat at Highbury in the Lancashire derby in League One.
It was former striker Carlos Mendes Gomes, playing against Morecambe for the first time since he left the club after scoring the goal the clinched promotion from League Two, who scored the only goal of the contest on 13 minutes.
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Shaun Rooney found space down the flank and picked out Mendes Gomes from the right who side footed home from close range at the near post.
Morecambe came close to an equaliser eight minutes later, when Dan Crowley’s cross from the left was headed onto the bar by Michael Mellon.
Late in the first half Liam Gibson denied The Cods a second when Rooney’s goal-bound strike was kept out on the goal line.
Connor Ripley made an excellent save to deny the hosts a second early on in the second half when he turned Rooney’s shot around the post.
Substitute Ash Hunter forced Fleetwood goalkeeper Jay Lynch into a good save with a powerful low effort, before Morecambe were denied a penalty five minutes from time, when Adam Mayor’s cross looked to have hit the arm of Rooney inside the area, but referee Andy Davies waved away the appeals.
Fleetwood who held on to take all three points, while the Shrimps remain outside of the relegation zone on goal difference.
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