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Gillingham’s run without a league win was stretched to five games on Saturday.
Wimbledon striker James Hanson went closest to opening the scoring during a disappointing opening half for the Gills.
Joe Pigott put the visitors ahead early in the second, a goal which turned out to be the winner, as the Gills struggled throughout.
Gillingham were facing a Wimbledon side who hadn’t enjoyed league success since the opening weekend.
The Dons side included four former Gills players in their starting XI. Deji Oshilaja captained the visitors, starting alongside Andy Barcham, Scott Wagstaff and Pigott, the latter having a brief loan spell at the club.
Barry Fuller, who has captained both teams to play-off success at Wembley, seven years apart, played right-back ahead of Luke O’Neill.
It was a scrappy opening half from the Gills, unable to produce any real quality and leaving visiting keeper Tom King with just a couple of routine saves, both coming from Tom Eaves headers.
Wimbledon had the better of the first half and went closest to scoring when Hanson rattled the bar. The follow-up from Pigott was saved by Tomas Holy. The Gills continued to be on the backfoot, with boss Steve Lovell shuffling his side around with a trio of different formations, without success.
The Dons had a penalty claim turned down, when Wagstaff went over in the box from a Callum Reilly challenge, and there were also calls for Brandon Hanlan to be shown a red card after his early tackle on Oshilaja.
Lovell made a double change at the break, introducing Elliott List and Luke O’Neill to the action. Eaves put an early header wide.
Wimbledon took the lead on 53 minutes. Pigott fended off Alex Lacey, running onto a ball over the top, and scored with a composed finish after taking it around keeper Tomas Holy.
The Gills upped the tempo midway through the half but visiting keeper King remained untroubled, as the Dons crowded them out.
Liam Trotter and Ben Purrington put speculative efforts well wide for the visitors while in needed a great clearance at the other end from Oshilaja to keep the Gills at bay, clearing with a bicycle kick as Eaves looked to pounce on a cross.
Byrne tried something spectacular in the Wimbledon box as well, but his overhead kick wasn’t anywhere near the target.
Wimbledon were trying to eat up minutes from early on, with numerous stoppages not helping Gills’ hopes.
There were calls for a penalty in the fifth minute of stoppage-time, as Ehmer went down in the box, but the referee ignored the appeals. Moments later an O’Neill free-kick was saved, the first time King had really been called upon.
Gillingham: Holy, Fuller, Garmston, Lacey, Ehmer, Byrne, Rees (O’Neill 46mins), Reilly, Wilkinson, Hanlan (List 46mins), Eaves. Subs: Hadler, Nasseri, Oldaker, Mbo, Ogilvie.
Wimbledon: King, Watson, Purrington, Oshilaja, Wagstaff (Pinnock 75mins), Trotter, Barcham, Hanson (Appiah 60mins), Soares (Wordsworth 70mins), McDonald, Pigott. Subs: McDonnell, Nightingale, Jervis, Sibbick.
Attendance: 5,246 (963 away)