The veteran midfielder produced a stunning right-foot curler from the edge of the area 15 minutes from time to give Accrington their 10th win in 13 games against the Shrimps.
Accrington took the lead in the 34th minute when Craig Lindfield’s cross found Kevin Long and his header was parried by Barry Roche into the path of Jayden Stockley who slammed the ball in from close range.
Andy Proctor went close to adding a second after 42 minutes with a shot from 25 yards that flew just wide of the right-hand post.
The Shrimps hit back with an equaliser in the 55th minute. Will Haining delivered a cross from the right which was met by Danny Carlton and his effort was well blocked by Ian Dunbavin but the ball fell neatly for Stewart Drummond to score from eight yards out.
Morecambe then enjoyed a period of dominance with Dunbavin saving well from Laurence Wilson and Lewis Alessandra before Hughes produced the all important moment of quality.