In 2005–06, Jones started in all but one of Wales's Autumn Internationals (he missed the game against ) and in all their 2006 Six Nations Championship matches, following which he was chosen by new coach Gareth Jenkins to captain the side during a mid-year two-Test tour of Argentina. In October 2006, Jenkins appointed Stephen Jones to captain Wales through to the 2007 Rugby World Cup, but when Stephen Jones was rested for the Autumn International against the Pacific Islanders, Duncan Jones returned to captain Wales at home for the first time. He played, as starter or substitute, in all four Autumn Internationals and all five matches in the 2007 Six Nations Championship, but was rested for the mid-year tour to Australia.