Neoentomelas asatoi Hasegawa, 1989 is a parasitic nematode that infests only the scincid lizard Ateuchosaurus pellopleurus (Hallowell, 1861) that inhabits the forest floor in the Northern and Central Ryukyu Archipelago, Japan. As a member of Rhabdiasidae, the reproductive mode of N. asatoi is characterised by the alternation of the protandrous hermaphroditic mode and gonochoristic mode throughout the life cycle. The intrafamily phylogenetic position and intraspecific diversity of this nematode species were inferred by molecular phylogenetic analyses. The results revealed the phylogenetic distinctiveness of Neoentomelas Hasegawa, 1989 in Rhabdiasidae that supports the unique generic status of Neoentomelas within the family. The intraspecific phylogenetic analyses of N. asatoi revealed a minor concordant phylogenetic pattern with the host and mosaic geographic arrangement of the major clades that was discordant with the host. The analyses and distribution pattern of subclades suggested that this geographic arrangement can be explained by at least three dispersal events and subsequent switching to indigenous host populations. Colonisation events might be promoted by the high establishment rate of new populations stemming from the parthenogenesis-like reproduction mode of N. asatoi. This study demonstrated that reproductive modes can affect the intraspecific genetic diversity of parasites.