Born in Bangor, Gwynedd, Hughes began his career at Bury where he was in the youth team.
He played in central defence for the club in six years between 1991 and 1997 making 202 appearances in all competitions for the Shakers and scoring two goals.
He became the Seasiders' club captain wearing the number 5 shirt[1] making 191 appearances in total, scoring six goals between 1997 and 2003.
In the 2000–01 season he scored in the Third Division Play-Off final at the Millennium Stadium in Cardiff as the Seasiders beat Leyton Orient to earn promotion.
[2] The following season, he helped Blackpool win the Football League Trophy at the same venue, playing as a substitute in the final.