In 2003, regional rugby came to Wales and Bowen and Jones were named as the two fly-halves for the Llanelli-based region, the Llanelli Scarlets; however, the start of the 2003–04 season coincided with the 2003 Rugby World Cup in Australia, which meant Jones was unavailable and Bowen started at fly-half for the first 10 games in the history of the Scarlets. Jones returned from the World Cup as first-choice, but the 2004 Six Nations Championship meant Bowen had another run in the team before the end of the season and he signed a new contract with the Scarlets in April 2004. Jones left for French side Clermont in the summer of 2004, and failed moves for New Zealander Andrew Mehrtens and France's Gérald Merceron meant Bowen was now considered the Scarlets' first-choice fly-half, although the newly signed Arwel Thomas and the young Ceiron Thomas challenged him for the starting position at various points in the 2004–05 season.