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A second-half penalty saw Ebbsfleet progress to the third round of the FA Trophy on Saturday.
Fleet had to play three quarters of the game with 10 men after Andre Blackman was sent off in the first half.
But they kept their shape well, dug deep and managed to triumph against the National League North leaders thanks to substitute Ayo Obileye's spot-kick.
Fleet made five changes from the team that lost at Barrow last weekend, with midweek signings David Gregory and Jermaine McGlashan among those who came into the team.
McGlashan was a class apart for the home side. Even when they went down to 10 men, he still put in a great shift and the ball was stuck to him seemingly on a piece of string at times.
Lynn should have taken a fifth-minute lead when Sonny Carey’s corner saw debutant Gregory parry Ross Barrows header but Adam Marriott somehow turned the loose ball wide from close range.
Marriott was at the centre of controversy in the 15th minute when visiting skipper Ryan Jarvis agreed to kick the ball back to Gregory after a clash of heads. But Marriott didn’t realise and played on, the move eventually seeing Lynn miss the target, although the reaction of visiting boss Ian Culvershouse suggested that the visitors may well have let Fleet walk in an equaliser had they inadvertently scored.
The flashpoint came midway through the first half when Blackman saw red. Jarvis was again in the action when he challenged home captain Josh Payne.
That led to a melee between the teams with Blackman sent-off for an off the ball incident with Barrows. Jarvis escaped punishment for his part.
Fleet replaced Alfie Egan with Ayo Obileye and it needed Lawrie Wilson to clear off the line after Gregory half-saved from Alfie Payne.
Ebbsfleet took 37 minutes to register a clear effort on goal, but Obileye’s header from John Goddard’s free-kick lacked any power.
Josh Umerah burst clear moments later but shot straight at keeper Alex Street from the edge of the area.
The start of the second half was best remembered for a flurry of yellow cards from referee Adrian Quelch. Fleet’s Josh Payne and Frankie Sutherland joining Lynn’s Jarvis and Barrows in the book - all for fouls near the halfway line.
Fleet made the breakthrough midway through the second half. Umerah chased a lost cause and when Chris Smith’s slip let him in, the striker advanced into the area. Smith got back but could only bring Umerah down to concede a spot-kick.
Obileye took over penalty duties and duly sent keeper Street the wrong way from 12 yards to put Ebbsfleet ahead.
Thereafter Ebbsfleet kept their shape well and it was Lynn who ran out of ideas, looking more disjointed after they made three changes in the second half, including the introduction of former Ebbsfleet forward Michael Gash.
Infact, the visitors never managed a shot on target in the second half - a measure of how well the Fleet defended.
Ebbsfleet: Gregory, Wilson, Ekpiteta, Grimes, Blackman, Sutherland, J Payne, Goddard, Egan (Obileye 29mins), Umerah (Adeloye 77mins), McGlashan. Subs not used: Palmer, Achuba, Dainkeh.
King’s Lynn: Street, Jones, Fox, Jarvis, Barrows, Smith, Carey (Limb 61mins), A Payne, Hawkins (Stewart 79mins), Marriott (Gash 63mins), Henderson. Sub not used: Kelly.
Attendance: 680.