Marrero spent the 2006 season with the GCL Nationals, Washington's affiliate in the rookie-level Gulf Coast League. In 2007, he played on Potomac Nationals, a high A team where he hit third spot and played first base. He began the 2008 season with the extended spring training team from the Washington Nationals and eventually ended up playing for the Potomac Nationals again. His second minor league season was cut short when he suffered a broken right fibula on 18 June 2008.