Sam Parkin opened the scoring after 15 minutes when he headed the ball past the advancing Colchester 'keeper to run the ball into the empty net.
Five minutes later Swindon had the ball in the back of the net again, but after Parkin was shooting the referee blew his whistle for hand ball, and disallowed the goal.
Mooney also came close to scoring in the first half, as Swindon piled on the pressure.
A minute after half time Mooney scored his 4th goal of 2004 with a close range header from a Brain Howard cross.
Colchester had few scoring chances throughout the game. There best chances came from a number of free kicks, some going over, but in the second half Colchester did hit the post following a free kick on the edge of the box, but that was the closest they came all game.
Jerel Ifil had a good game, although he did pick up a yellow card in the first half with a late tackle. This was Ifil's last game for Swindon, and by the second half the Town End fans were calling for King to "Sign Him On".
Overall a deserved 2-0 win. Colchester never really looked like they would score, and Swindon did have chances to get a few more goals in the first half.
Next weekend Swindon travel to play Notts County who they beat 4-0 at the County Ground earlier in the season.