Hughes was born in St Albans and, after playing youth football with Weymouth, joined Southampton in March 1991, initially as a trainee.
He signed a professional contract in August 1991, but did not make his first-team debut until 5 February 1994 (in a 2–1 defeat away to Oldham Athletic) shortly after the appointment of Alan Ball as Saints' manager.
In his nine years at The Dell he suffered an incredible catalogue of injuries including broken legs (twice), fractured ribs and back problems which required surgery.
[1] He was a rare goal-scorer, but scored twice in consecutive matches, firstly away to Queens Park Rangers on 28 December 1994 with an acrobatic scissors-kick, and again at home to Manchester United three days later with a right-foot shot, both games ending 2–2.
[3] His career at Southampton finally ended after a knee injury picked up in the August 2000 pre-season at Aldershot.