Márquez was selected by Ricardo La Volpe for the 2006 World Cup in Germany. Márquez played in all of three of Mexico's opening round matches, and scored the lone Mexican goal in a 2–1 loss to Argentina in the second round off a Pável Pardo free kick which was headed to the far post by Mario Méndez, allowing an unmarked Márquez to strike the ball into the back of the net. The winner was scored by Maxi Rodríguez in extra time after Hernán Crespo had equalised for Argentina.