With the returning Paul Rowlands in the starting line-up Glan began brightly with Richard F Owen attempting to beat the keeper with a long range effort and Kevin Roberts glancing header from a Darren Jones cross going wide in the opening five minutes. Playing with a strong breeze behind them on a lively pitch Glantraeth were more than matching the home side but fell behind on 23 minutes as Simon Hulse got behind the defence and finished powerfully.
Isa were playing a dangerous game pushing up almost to the half-way line looking for offside but Glan were failing to take advantage although they were hardly helped by an assistant referee who was raising his flag far too quickly rather than waiting to see how play developed.
Twelve minutes before the break Isa took firm control as a scramble around the Glantraeth goal following a right wing corner ended with ex-Llangefni striker Chris Boulton poking the ball home.
Kevin Roberts had a shot on goal comfortably saved and a long distance effort from Chris Saxon saw the keeper scrambling to save as Glantraeth began the second period looking to get back in the game but their fate looked to be sealed on 56 minutes as a well struck shot by Nathan Jones entered the net off the inside of a post.
There was a glimmer of hope for the visitors after 77 minutes as a hand ball in the area led to a penalty that was well converted by Gerallt Jones. At last Glan sprung to life and a jittery home defence was now under real pressure with Gerallt Jones testing the keeper with a fierce shot from ten yards then Gareth Owen heading narrowly wide of a post from the resulting corner.
Subsitute keeper Richard Hall did well with six minutes remaining to save from Hulse as the Isa forward was clean through on goal.
It was a disappointing to go out of the Welsh Cup at the first round stage for the second successive season but over the 90 minutes Glan had not set the home defence enough problems and can have few complaints about the result.
Glantraeth: Gareth Hughes (Richard Hall 66), Jason Thomas, Darren Jones (Andy Tower 58), Llion Davies, Gareth Owen, Richard F Owen, Paul Rowlands, Chris Saxon, Gerallt Jones, Kevin Roberts (Alan Jones 61), Emyr Rowlands.