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Oldham made Gillingham pay for their first half misses after taking maximum points at Boundary Park.
Gillingham fell behind to a first-half strike from Gary Harkins and the hosts also hit the post.
The Gills had been unable to make the most of their numerous first half chances and those opportunities dried up for the visitors after the break, with home keeper Mark Oxley in top form when called upon.
Both Oldham and Gillingham went into the match chasing mid-table comfort. Defeat was the Gills’ second in a row.
The men from Kent started the match with their top scorer, Cody McDonald, surprisingly on the bench.
Boss Peter Taylor instead started the match with Charlton loanee Joe Pigott upfront, with Craig Fagan and Chris Whelpdale providing assistant from out wide, in a 4-5-1 formation.
There were six changes for the Gills in total to the eleven which started the midweek match against Sheffield United. Bradley Dack and Michael Harriman missed out completely.
Gillingham weren’t short of chances in the opening 45 minutes, with Connor Smith pulling the strings just behind striker Pigott.
But Taylor’s men were made to pay for missed chances as Harkins fired home after 33 minutes from a tight angle. The Gills defence, possibly expecting a cross, were caught off-guard.
Just two minutes earlier Myles Weston – on for injured Whelpdale – was denied by Oxley after finding himself one-on-one with the home keeper.
Prior to that Oxley had also saved a low Smith shot and seen chances from Whelpdale and Fagan go wide. Jake Hessenthaler also came close, finding the roof of the net with a cheeky chip.
The Gills came close to an equaliser twice before the break, with Smith firing one effort into the side-netting and seeing another saved one-handed by Oxley.
Oldham still could have doubled the lead before the whistle for the break went, inbetween Smith’s efforts, and it was referee Mike Russell who created the chance. Russell ran into Fagan, dispossessing the Gills man, and as the ball ran loose Jon Stead cracked a low effort against the base of the post. 1-0 it ended at the break.
Gillingham offered little going forward in the second half and on the hour Taylor made a switch, with McDonald and Adebayo Akinfenwa going on.
Oxley remained untroubled, however, with Akinfenwa heading over and Myles Weston smashing a shot wide with 17 minutes left.
The home keeper continued to frustrate the visitors and with four minutes left he made a diving save to deny Akinfenwa, after the Gills man turned and shot on the edge of the box.
Gillingham: Nelson, Martin, Hewitt, Legge, Barrett, Gregory, Hessenthaler (McDonald 59mins), Whelpdale (Weston 25mins), Smith, Fagan, Pigott (Akinfenwa 59mins). Subs: Linganzi, Davies, Lee, Baxter.
Oldham: Oxley, Brown (Dayton 75mins), Grounds, Wesolowski, Stead, Winchester (Dunfield 75mins), Wilson, Lockwood, Philliskirk (MacDonald 81mins), Worrall, Harkins. Subs: Mellor, Kissock, Turner, Rachubka.
Attendance: 3,714