In 2006, Parrish led the Mud Hens to a 76–66 record and a repeat of the Governor's Cup, giving the Mud Hens their third title and making them back-to-back champions for the first time in team history. This time, the Mud Hens defeated the Rochester Red Wings. The team moved on to play in the first Triple-A Baseball National Championship Game, in Oklahoma City, where they would take on the Tucson Sidewinders of the Pacific Coast League. The Mud Hens fell to the Sidewinders by a score of 5–2.