This achievement made him the first ever Mexican football player ever to ever win this competition, something Hugo Sánchez was not able to do during his time in La Liga with Real Madrid. After the 2006 FIFA World Cup, Barcelona extended his contract for the following 4 years to €38.5 million which will see his contract end in June 2010. Despite sustaining injuries, he was rumored to be up for sale at the end of the 2006-07 season. His future at Barça was up in the air until the 2007 Copa America, where Márquez regained his best form and was one of the best players of the competition, helping Mexico to an acceptable 3rd place.

In the 2007-08 season, Márquez got off to an excellent start, as he managed to form a solid partnership with new signing Gabriel Milito while captain Carles Puyol was out injured. However, constant injuries threw off his form. Márquez's success declined with the rest of the season leading Barcelona to end up in 3rd place after a miserable second half where injuries lead to his contribution being negligible. Even so, it appears new coach Josep Guardiola will continue to rely on his contributions; with the departure of Ronaldinho, Márquez has become the last original signing of the Rijkaard era to remain on the team. He appears to be Guardiola's first choice at center back along with captain Puyol for the 2008-09 season. On 13 December 2008, Márquez played his 200th match for Barcelona in the clash against Real Madrid, which they won 2-0. On 28 April 2009, Márquez got injured in a match against Chelsea in the semi-final of the Champions League. Márquez was told he needed surgery on his left knee, forcing him to miss the rest of the season. Barcelona would go on to win a historic treble after winning the 2008–09 UEFA Champions League, in which Márquez was present but was sidelined. Márquez also received an offer from Italian side Fiorentina. However, Márquez admits he would like to end his career at Barcelona and insists he is not concerned about the fact that his current contract runs out during the summer of 2010. Márquez signed a new contract with Barca in November 2009 that will keep him at the club until 2012. His buy-out clause is $150.4 Million. On February 20, 2010, he scored his first goal since his return against Racing Santander.

Since making his international debut on 5 February 1997 against Ecuador, but was not chosen for the 1998 FIFA World Cup squad. Márquez has been one of the Mexican national football team's most important players. Márquez has played various tournament's with the Mexican team, winning the 1999 FIFA Confederations Cup and the CONCACAF Gold Cup. Márquez started all four of Mexico's games during the 2002 FIFA World Cup in Korea/Japan, where he was given the Captain's Armband by then coach Javier Aguirre despite his young age of 23. Despite a strong performance during the group stage of the tournament, he received a red card during Mexico's second round 2-0 loss to the United States for a deliberate midair head butt on Cobi Jones in the final minutes of the match. Márquez was an integral part of Mexico's subsequent World Cup qualification campaign and was selected by Argentine coach Ricardo Lavolpe for the 2006 FIFA World Cup in Germany.

During the 2006 FIFA World Cup, Márquez played in all of four 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 Rodriguez in extra time after Hernan Crespo had equalised for Argentina. Since Mexico's second round exit, he has spoken out about the need to encourage future Mexican football players to play in Europe to increase the competitiveness of the team.