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Peter Taylor’s interim reign started with a goalless draw at Priestfield.
Both teams struggled for clear-cut chances but Gills keeper Tomas Holy was the busier of the two.
Tom Hopper had the best chance of the night, with two minutes left, but was denied by Holy.
Taylor was back in charge for Tuesday’s game, on a temporary basis, and there were a few surprises in his chosen XI.
Regular strikers Conor Wilkinson (hip) and Tom Eaves (suspension) were missing but Taylor opted to select youngsters Elliot List upfront, with support from Sheffield Wednesday loanee Sean Clare.
Six recognised defenders started the match, along with defensive-minded midfielders Jake Hessenthaler and Mark Byrne. Holy kept his place in goal and there was no recall to the squad for Stuart Nelson.
List was making his first start of the season and if his inclusion was a surprise for Gills fans, it was probably more so to Scunthorpe, who looked troubled by the youngsters pace early on.
It was List who nearly engineered the Gills an early breakthrough, bursting into the box and putting some pace on his cross, narrowly missing contact with the onrushing Clare.
Taylor started the match with wing-backs but an early injury to Luke O’Neill led to a switch in formation, with Josh Parker going upfront and Clare operating at the top of a midfield diamond, in a 4-4-2 system.
The Gills managed to nullify much of Scunthorpe’s attacking threat while showing some encouraging signs themselves up top, with List a menace at times. He nearly sent Parker away on goal midway through half, taking just a fraction too long before sending his team-mate in.
Clare’s corner towards the end of the half came close to unlocking the Scunthorpe defence – one that had only conceded three in the league before Tuesday night. Ehmer flicked the ball on for Alex Lacey at the back post but he couldn’t find the target on the stretch.
Gillingham finished the half without a shot on target but looked more of a threat than they had at the weekend. Another formation change for the second half saw Jesse Starkey introduced for Clare as Gills went for four across the middle.
Duane Holmes had the game’s first on-target shot early in the second half, but Holy saved with his legs. With just over an hour gone the Gills had their first shot on target, but Byrne’s floated effort didn’t trouble the keeper.
Holy saved from Josh Morris and Lee Novak put a chance wide for the visitors, inbetween an effort from Parker that missed the Scunthorpe goal by some distance. Murray Wallace headed a good chance wide late on for the visitors.
It needed another Holy save late on, denying Hopper, to keep the scores level. The game came to life in the closing stages and Starkey had a deflected shot go narrowly over at the other end.
Gillingham: Holy, O'Neill (Parker 17mins), Ogilvie, Lacey, Nugent, Zakuani, Ehmer, Hessenthaler, Byrne, Clare (Starkey 46mins), List (Nash 70mins). Subs not used: Arnold, Oldaker, Simpson, Cundle, Starkey.
Scunthorpe: Gilks, Clarke, Butroid, Wallace, McArdle, Bishop, Ojo (Manton 64mins), Holmes (Adelakun 85mins), Morris, Madden (Novak 64mins), Hopper. Subs not used: Watson, Crofts, Van Veen, Burgess.
Attendance: 4,002 (158 away)