 They finished second in the 2006 Clausura tournament, their best result ever, reaching the final and eliminated by the defending champion Municipal.Marquense qualified to the UNCAF Club Tournament for the first time in their history after finishing above the loser of the 2005 Apertura final, Comunicaciones, in the overall standings.The team reached the semi-finals of the 2006 UNCAF tournament, where they lost to Costa Rican club Puntarenas, but after beating Victoria of Honduras in the third place match on a 4–1 aggregate, they were able to reach the CONCACAF Champions' Cup for the first time in their history.