Márquez began his career with Atlas in 1996, playing in over 70 games with the club before moving to France in 1999 with Monaco, where he won the Ligue 1 title. In 2003, Márquez transferred to FC Barcelona, becoming the first ever Mexican to represent the club. He would go on to play in over 200 games during seven seasons with the "Blaugrana", and win numerous championships. In 2006, he became the first Mexican player to win the UEFA Champions League when Barcelona defeated Arsenal in the final. In 2010, Márquez joined the New York Red Bulls of Major League Soccer. After being released from the club in 2012, he moved back to Mexico, this time to play for Club León, captaining the team to back-to-back Liga MX titles in 2013 and 2014. Márquez then transferred to Hellas Verona of the Italian Serie A. He returned to boyhood club Atlas in 2015, and announced his retirement from football in April 2018.