Barnet were undone by a goal in each half and despite rallying to equalise with half-time approaching, the home side took control of much of the proceedings in the second period and ran out worthy winners.
Barnet had however carved out some reasonable goalscoring chances, and had they been taken the story might have been different, but it cannot be denied that Morecambe deserved the three points.
Ian Hendon welcomed back Gary Breen at centre-back, with Ismail Yakubu not sufficiently recovering from a strain, Daniel Leach partnered the assistant manager.
Matt Lockwood was at left-back, Lee Sawyer started on the right of midfield, Albert Adomah on the bench, Paul Furlong and Jake Hyde were the strike partnership.
Before the game could settle into a pattern Morecambe took the lead. In only the 4th minute Mark Duffy delivered a teasing cross which Stewart Drummond, advancing from midfield, powered a header past Jake Cole.
Barnet immediately responded with Lockwood being set up by Jake Hyde for a one-on-one with the home goalkeeper, this effort being saved, with both Sawyer and Furlong going close from the following series of rebounds.
Drummond in midfield for the Shrimps was spreading the play and retaining possession and Wayne Curtis nearly extended the home side's advantage on 9 minutes when his effort flashed wide of a post.
Sawyer was seeing a lot of the ball, not limiting himself to the right wing and was influential when Barnet did take the game to Morecambe.
On the half hour Ian Hendon make a tactical switch; Adomah was introduced on the flank with Sawyer moving inside, Micah Hyde being substituted.
Within three minutes the Bees were level. Mark Hughes was grounded as he was about the shoot when well positioned. Up stepped Lockwood to confidently put away the spot kick.
Barnet then enjoyed their best spell of the match. In time added on in the first half Adomah swept past three defenders with Furlong then having the time to steady himself at the edge of the box, but his shot was wide of the target. A genuine opportunity.
Barnet were on the receiving end in much of the second period, but as the clock ticked down it looked increasingly as if the Bees would be able to hold onto a point, perhaps even sneaking something more.
Yet the fact that Craig Stanley had hit the cross bar on 70 minutes and that Drummond had had an opportunity were portents of what would eventually happen.
In the 78th minute Breen looked to have been fouled with Duffy capitalising, taking the ball goalwards and firing past Cole from an angle.
Immediately Barnet sought an equaliser with Adomah delivering the ball into the box, the ball falling to O'Flynn, but Furlong had been ruled offside.
Morecambe were now in no mood to relinquish their advantage and comfortably held Barnet at bay, indeed Michael Twiss and Duffy both had efforts hit the woodwork.
The Bees are at home to Torquay United on Tuesday, a game that Ian Hendon has classified as "massive".
David Bloomfield.