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Gillingham should have won by more in a game they dominated at Priestfield.
Mikael Mandron put the Gills ahead with a first-half volley and were rarely troubled by the visitors.
Lincoln were under plenty of pressure after the break, with Mandron hitting the woodwork among a sea of chances, but the Gills couldn’t extend that lead.
Gillingham boss Steve Evans made just one enforced change to the side which played Sunderland, with left-back Tom O’Connor away on international duty. Midweek goalscorer Jack Tucker was returned to the XI.
Only goal difference separated the sides prior to kick off, with the Gills just ahead in the table.
The match struggled to take off but Mandron capped an impressive start personally with he opening goal in the 24th minute.
Mark Byrne’s ball in from the left was met by Lincoln defender Jason Shackell, he didn't get much of a contact, and there was Mandron to volley home from close range.
Prior to the goal the only real moment infront of either goal saw Stuart O’Keefe fire a rising shot at goal, which keeper Josh Vickers dealt with comfortably.
The Gills had edged the half but chances at goal were rare and Olly Lee blasted an effort over the bar.
Lincoln brought on big striker John Akinde to give them extra in attack for the second half after the Gills had comfortably contained lone striker Tyler Walker in the opening 45.
Lee twice fired well wide for the Gills as the hosts continued to look untroubled. O’Keefe also missed the target and Mandron headed a good chance over from Byrne’s cross.
The chances kept coming for the Gills and Brandon Hanlan couldn’t keep a header down from a Lee cross.
Mandron glanced a header onto the bar with 20 minutes left and Hanlan was denied as he looked to pull the trigger, thanks to a timely challenge. Hanlan was denied again moments later, by Neal Eardley, taking a great first touch but seeing his shot blocked by the Lincoln defender.
The Imps twice went close late on, Akinde with a glancing header and Bonham turning over Walker's header in stoppage-time.
Gillingham: Bonham, Tucker, Fuller, Ehmer, Ogilvie, Jones, Byrne, O’Keefe, Lee (Charles-Cook 90mins), Hanlan (Jakubiak 90mins), Mandron. Subs not used: Walsh, Hodson, Ndjoli, Cisse, Marshall.
Lincoln City: Vickers, Toffolo, Shackell, Pett, Payne (Anderson 69mins), Andrade, Chapman, Walker, Connolly (Bolger 46mins), Eardley, Hesketh (Akinde 46mins) Subs not used: Smith, Frecklington, Grant, Melbourne.
Attendance: 5,567 (453 away)