The history of the Highlanders focuses on the rugby union team in the Super Rugby competitions. The team was originally formed as one of five New Zealand franchises for the Super 12 in 1996. The team encompassed the provinces of North Otago, Otago and Southland. The Highlanders placed eighth in their first year with five wins, but slumped to last in the competition in 1997 with only three wins. They improved to qualify for their first semi-final in 1998, and became the first New Zealand team to defeat all four South African franchises in the process. They were defeated by eventual 1998 Champions the Auckland Blues in their semi-final however. Their best ever finish came in 1999 when they won eight matches, and their semi-final to host the 1999 Super 12 Final at Carisbrook, but lost to South Island rivals Crusaders in the match. They qualified for their third consecutive semi-finals in 2000, and this time played the Crusaders in Christchurch, but lost again.
In 2001 they could not repeat a play-off performance, they did finish fifth and maintain an unbeaten record at Carisbrook for the second season in a row. In 2002 the Gordon Hunter Memorial Trophy was introduced to be contested with the Blues, and the Highlanders won the trophy with a 20–13 win at Eden Park. They did this on their way to finishing fourth, before again losing to the Crusaders in their semi-final. In 2003 they lost their first match at Carisbrook since the 1999 Super 12 final when the Crusaders defeated them 17–16. Coach Laurie Mains resigned at the end of that season after a dispute with some of the senior players, including Anton Oliver. In 2004, their first season with coach Greg Cooper, they finished ninth despite scoring more tries then in 2003. This was mainly due to their defence as they conceded 12 more tries then in 2003. Despite winning six consecutive games in 2005, they eventually finished eighth due to losing their last three matches.
After the expansion of the Super 12 to the Super 14 with the addition of two teams—one each from Australia and South Africa. In both the 2006 and 2007 seasons the Highlander's finished ninth with 27 competition points when they won six and five matches respectively. Following their 2007 season coach Greg Cooper left the franchise, and was replaced by Glenn Moore. Moore coached the team for three seasons, but achieved only ten wins during that time, and finished no higher than ninth. Jamie Joseph was appointed coach for the 2011 season, and under him finished eighth that season, and ninth the following year.