Mark Jones began his domestic career at Builth Wells Youth before joining the senior side. He was signed by Llandovery from Builth and in his first season of senior rugby was the highest try scorer in the Welsh League. Jones joined Llanelli in 1997 and will remain with the Scarlets until 2010, after he signed a three year contract extension with the region in the summer of 2007.

Jones has represented Wales at U18, U19 and U21 levels and made his first team debut for Wales as a replacement against England in the 2001 Lloyds TSB Six Nations.

2005–2006 was a great season for Jones, as he won six international caps and scored three tries. This was after consecutive knee injuries, and major reconstructive surgery, saw him ruled out of the international arena since the 2003 Rugby World Cup.

Jones scored seven tries for the Scarlets during the 2006–2007 season, three of which came in the region's Heineken Cup endeavour, including one in the semi-final loss to the Leicester Tigers.

Jones appeared for Wales in the RBS 2007 Six Nations against Scotland, Italy and in the sole victory over England. In June, Jones was named named in Gareth Jenkins's 41-man preliminary Rugby World Cup 2007 summer training squad after being rested from the two Test tour to Australia. Jones made the final 30-man cut for the RWC squad in August and played in Wales's Invesco Perpetual Summer Series, scoring a try against Argentina.

Jones appeaed for Wales in the Rugby World Cup in Pool matches against Canada and Australia. He also played in the final Pool B encounter, scoring a try in Wales's defeat at the hands of the Fijians. In November 2007 Jones was selected by Caretaker Coach Nigel Davies in the line-up to face world champions South Africa in the Prince William Cup at the Millennium Stadium.

New Wales Coach Warren Gatland included Jones in his Grand Slam winning 2008 RBS Six Nations squad. He played in four matches, against England, Italy, Ireland and France, and almost scored a try for his country in the latter championship decider against France, being stopped just short of the line after a superb break.

Jones figured in both summer internationals against South Africa and also figured against Canada and Australia in the autumn. He played against England at the Millennium Stadium and Italy in Rome in the 2009 RBS 6 Nations and played against USA on the Wales tour of North America. He was named captain of the Scarlets for the 2009-10 season.