 Following the 2005 – 06 season, Horton's rookie contract expired. He was re-signed by Florida on July 12, 2006, to a one-year, $ 1.1 million contract. Against the Boston Bruins, Horton scored his first goal of the season to help the Panthers win 8 – 3. He scored his third goal of the season on October 18 in a 5 – 2 loss against the Washington Capitals, who the Panthers had not lost to in regulation since the 2004 – 05 season. After Horton was called for a second-period penalty against Atlanta, coach Jacques Martin demoted Horton to the fourth line in an attempt to send a message to Horton. Before long, however, Horton was again promoted to the first line, with Finnish players Olli Jokinen and Ville Peltonen. They gave Horton the name "Nathan Hortonen" in an attempt to make his name Finnish. Against the Montreal Canadiens on November 16, Horton assisted on all goals that Jokinen recorded. Against Tampa Bay on February 17, Horton scored the game-winning goal for Florida, 29 seconds into overtime.
