Another game, another away defeat for the Gills who failed to take their chances at the Globe Arena.
Garry Hunter gave the home side the lead as early as the eighth minute and despite Gillingham battling hard they went two down on 68 minutes when substitute Kevin Ellison fired home.
There was still time for a consolation as Frank Nouble scored a 95th minute penalty after Jo Kuffour was upended in the box by Morecambe keeper Barry Roche.
Gills boss Andy Hessenthaler elected to keep faith with the side that lost 2-0 to Swindon Town on Tuesday night, despite having Danny Kedwell and Joe Martin available on the bench.
Jim Bentley’s Morecambe side got off to the perfect start when Garry Hunter scored his first goal of the season after only eight minutes. Hunter received the ball on the edge of the area and produced a superb, dipping volley which beat Ross Flitney as it went in off the crossbar.
Gillingham hit back and enjoyed a large share of possession without producing too many threatening moments. Luke Rooney looked the visitors’ most lively player and finally tested Barry Roche on the half-hour with a save at his near post after Chris Whelpdale had fired wide.
The second half continued in much the same way, with Gillingham seeing a lot of the ball but being held at arm’s length by some excellent Morecambe defending. That solid platform proved vital as Morecambe added a second on the break. Stewart Drummond found Izak Reid down the left with a superb ball and the wide man teed up Ellison, who produced a fine finish from 12 yards to double the Shrimps’ advantage.
Gillingham finally broke the Shrimps’ defence in injury time when they won a penalty after Roche had brought down Joe Kuffour in the box. Frank Nouble slotted home the spot kick but the final whistle went seconds later as the Shrimps held on for a welcome three points.
FULL TIME: MORECAMBE 2-1 GILLINGHAM
Saturday’s defeat sees the Gills drop to 10th in League Two, five points behind Morecambe who move into third and next up for Andy Hessenthaler’s side is Northampton Town at Priestfield next Saturday.
Morecambe line up: Roche, Haining (Charnock 28), McCready, Wilson (Reid 49), Parrish, Hunter, Drummond, McDonald, Alessandra, Price (Ellison 62), Carlton.
Subs not used: Routledge, Fleming.
Goals: Hunter (8), Ellison (68).
Booked: Roche (94).
Gillingham line up: Flitney, Fish, Richards, Lawrence, Jackman, Whelpdale, Lee, Weston (Kedwell 58), Rooney (S Payne 79), Nouble, Kuffour.
Subs not used: Gazzaniga, Frampton, Martin.
Goal: Nouble (pen 95).
Referee: Mr Boyeson
Attendance: 2,067