"I don't think Lee played particularly well and I was thinking of taking him out of the game," admitted Megson.
"But that goal was typical of him. He has that wonderful sense of knowing where the ball is going to be and thankfully he was there to apply the finishing touch."
The shaven-headed Hughes guaranteed the all-important points for Megson's high-flyers and sent relegation-threatened Gilingham crashing to a fifth successive defeat - the club's worst run in 12 years.
Hughes pounced in the 78th minute to tap the ball home at the far post after substitute Lloyd Dyer had drilled a low hard ball into the heart of the Gillingham defence.
The goal earned Albion a sixth successive victory - their best run of the season - and maintained their eight-point cushion over third-placed Sunderland who have a game in hand.
"It was never going to be a nice open game," added Megson. "They packed their defence and sat deep. They tried to get a point and it looked for a long time as though they were going to get away with a point.
"We knew we needed to win just to stand still and it showed in the way we played.
Anybody who has been involved in a promotion-winning team will without a shadow of a doubt play in a game like that."Albion were frustrated for long periods by the delaying tactics of the Gills which resulted in nearly ten minutes of injury time being played at the end of the first half.
"There were a lot of players going down and the referee can't do anything but stop play," said Megson.
"With the way we were going I thought we were going to finish at 7.20pm!"
Andy Hessenthaler, the Gillingham player-manager, admitted they were disappointed to have got nothing from the game.
"We are in a relegation battle and I thought we worked our socks off," he said.
"We put a lot of effort into the game and we're absolutely gutted to have got nothing.
"This is an Albion team I am sure are going up to the Premiership so full credit to my boys.
"Now we have got to pick ourselves up because we have to play Walsall on Monday and that's the biggest game this club has been in for a long, long time.
"We have been ripped apart by injuries but I certainly believe, if we can keep playing like that, we will stay up."Hessenthaler concluded:
"That goal from Lee Hughes was a kick in the teeth. But that's how it has been going for us. It's that last bit of quality in the final furlong. That's what has been missing."
It was always Albion who held the edge but they found it difficult finding a way through the packed Gills defence with Sean Gregan having a left-footer saved by keeper Steve Banks in the 23rd minute.
Then after the break Paul Robinson blasted in a 20-yarder that flew just over the Gillingham woodwork before Jason Koumas beat two men only to have his low hard shot well-taken by the diving keeper.
Albion went close to breaking the deadlock in the 70th minute when Geoff Horsfield forced in a rising angled drive only for Banks to make a superb one-handed block at his near post.
Megson concluded: "We are still nowhere near to playing as well as I know we can play. But I said to my players before the match, 'First and foremost winning is everything'."