Márquez made his debut with Mexico on 5 February 1997 in a friendly match against Ecuador. It was reported that his call-up was due to an error made by national team coach Bora Milutinović, who wanted to call up fellow Atlas player César Márquez. Márquez became a regular call-up for Mexico, although he was not chosen for the 1998 FIFA World Cup squad. Márquez played various tournaments with the Mexican team, winning the 1999 FIFA Confederations Cup and losing to Canada at the 2000 CONCACAF Gold Cup. Márquez started all four of Mexico's games during the 2002 World Cup in South Korea and Japan, where he was given the captain's armband by then coach Javier Aguirre despite his young age of 23. He received a red card during Mexico's second round 2–0 loss to the United States for a deliberate mid-air head butt on Cobi Jones in the final minutes of the match.