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Lee Martin scored two super goals as the Gills won at Portsmouth for the first time in their history.
Jamal Lowe had put Portsmouth ahead but fluffed a great chance to make it two before the break.
Conor Wilkinson, on at the break, levelled just three minutes after the restart as the Gills put a poor opening half behind them.
Connor Ronan hit the post for the home side before Martin’s double put the Gills on the path to victory.
Illness got the better of both of Gillingham’s senior left-backs meaning Callum Reilly was chosen to fulfil the role.
Connor Ogilvie missed out completely while Bradley Garmston was on the bench.
Scott Wagstaff returned to the starting XI in a 4-2-3-1 formation but it was the home side who had the better of the first 45.
Gillingham were unable to capitalise on a couple of good early balls into the box from out wide, with the best of the chances falling at the other end. Lowe headed a cross wide and Kal Naismith also went close.
It was Lowe who opened the scoring, as the Gills failed to get a decent challenge on him inside the box. He managed to retain possession of the ball, after good work from Naismith and Dion Donohue, firing into the roof of the net.
The forward should have doubled the lead with 27 minutes gone, having plenty of time and space to beat Tomas Holy. After beating the offside trap, he delayed the finish and Luke O’Neill timed his tackle well to thwart him.
Tom Eaves was getting little joy upfront and the nearest the Gills got to scoring in the half was when defender Matt Clarke screwed his clearance goalwards, grateful to see keeper Luke McGee on hand to spare his blushes.
Eaves, who had been substituted before the break at Bury, didn’t make the second half at Portsmouth either. He made way for Conor Wilkinson at half time.
The Gills started the second half well, with Wagstaff having an early shot that hit a defender. Appeals for handball and a penalty were waved away by the referee.
Whatever the manager said at the break, it certainly worked. Gills were a different looking team.
Wilkinson had been involved in that early second half chance but then hit an equaliser moments later, outwitting the defender before firing curling the ball home.
Gillingham remained on the front foot but Ronan almost restored Portsmouth’s lead just before the hour, beating Holy with a free-kick but seeing it bounce clear off the upright.
Martin celebrated putting the Gills ahead on 66 minutes, whipping the ball in and seeing it nestle into the far corner, with Wilkinson in close attendance, doing enough to at least distract the keeper.
Portsmouth remained a threat, with Dion Donohue wasting a good chance and substitute Brandon Haunstrup heading at the keeper.
Just as Portsmouth were beginning to look more dangerous, Martin scored a fantastic third goal, bending home the ball from outside the box into the far corner.
Portsmouth: McGee, Walkes, Clarke, Burgess, Ronan, Whatmough (Chaplin 76mins), Donohue, Lowe, Naismith, Deslandes (Haunstrup 65mins), Close. Subs: Basss, Kennedy, May, Smith, Widdrington.
Gillingham: Holy, O’Neill, Ehmer, Zakuani, Reilly, Byrne, Hessenthaler, Martin (Nasseri 90mins), Wagstaff (List 79mins), Parker, Eaves (Wilkinson 46mins). Subs: Garmston, Nugent, Hadler, Moussa.
Attendance: 18,246 (1,551)