The millipede, Nemasoma varicorne, represents a textbook example of geographic parthenogenesis with thelytokous populations being distributed north, east, south and west of the distribution of the bisexual ancestor in the deciduous forests of central Europe. We here describe variation in amplified fragment length polymorphisms (AFLP's) in sympatric bisexual and thelytokous populations of N. varicorne in Denmark and compare the relationships of Danish populations with animals from The Czech Republic, England and Poland. Thelytokes from Denmark, England and Poland form a monophyletic cluster that differs from bisexuals from Denmark and Czechia for about 30% of the fragments. A single clone is widely spread over Denmark (34 of 38 localities), with rare clones being detected at four other localities. The phylogenetic pattern implies strongly that thelytoky evolved prior to the post-glacial colonization of northern Europe. This further suggests that the two forms have interacted extensively during this colonization and that the thelytokes have been excluded from older forests by competition with the bisexual forms. Our results further suggest that the success of the thelytokous form, at least in Denmark, is not due to abundant clonal diversity as hypothesized by the frozen niche variation model.