Holmes re-signed with the Jets during the offseason, shortly before the start of 2011 season agreeing to a 5-year deal. He was named one of the team captains, along with starting quarterback Mark Sanchez, before the season began. In the 4th quarter of the final game of the 2011 season against the Miami Dolphins, Holmes appeared to get into an argument with Jets offensive tackle Wayne Hunter while the team was huddling. As a result of the argument, Holmes was benched for the remainder of the game, and the Jets ended up losing the game, which resulted in the Jets missing the postseason for the first time in 3 years. His leadership qualities and credibility as a captain have since been questioned.