They were relegated down as the Segunda Division (third tier in the country), before earning promotion to the Primera División de Ascenso in the 1990s.

After more than three decades competing in lower divisions, the team was promoted to the Liga Nacional in May 2000, and they reached the semi-finals of the 2004 Apertura tournament.

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.

In the 2007 Clausura tournament, Marquense reached the final, facing rivals Xelajú, who won the title on a 4–2 aggregate score.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.