In May 2002, following Wimbledon FC's owners' attempts to relocate the club to Milton Keynes, Wimbledon Independent Supporters Association and The Dons Trust supported the formation of AFC Wimbledon. The vast majority of Wimbledon football fans regard AFC Wimbledon as the continuation of the original club. Also, the Wimbledon women's team, which plays in the regionalized second level of England's women's football pyramid, refused to move to Milton Keynes; it changed its affiliation to AFC Wimbledon after the 2002/03 season.

The Milton Keynes team, often derisively called "Franchise FC", has spent the bulk of the 2003/2004 season in last place, and under bankruptcy administration. It is most likely that Wimbledon FC will be competing in the English Second Division next season. It has been suggested that the club should change its name to reflect the area it is now based in, with Milton Keynes Dons being the most probable.

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