Mark joined Bray Wanderers U19 team from Belvedere FC ahead of the 2011/12 season.
Following a Scunthorpe United tour in Ireland in the summer of 2012, in which Mark played for "The Iron", he was signed by their manager Alan Knill in August.
Having made just one appearance for their Senior Team (in the Johnstone Paints trophy), he was released by incoming manager Brian Laws in January the following year. Season 2013 saw Mark signed by Roddy Collins for Athlone Town where he was part of the team that won the First Division title and promotion, playing in 26 league games and scoring twice.
He re-signed for Athlone for 2014 and made 26 appearances in the Premier Division that season.
Athlone were relegated and in 2015, Hughes signed for Alan Mathews at Drogheda United. After 25 league appearances for ‘Drogs’, they were relegated and Mark Hughes moved on, this time to Longford Town.
He made 23 league appearances for them, but suffered relegation for the second consecutive year, when Longford ended up last in the Premier.
He signed for Shelbourne in early March 2017 and made his debut in a 2-2 draw with Waterford on St. Patrick's Day.