There are close to 100 described gnathostomulid species, but many more times that number likely await discovery. Gnathostomulids were first described, in 1956, as turbellarian Platyhelminthes (free-living flatworms), but were given phylum rank in 1969. Recent work has supported the recognition of a monophyletic clade Gnathifera consisting of the clade Syndermata (Rotifera + Acanthocephala) plus the Gnathostomulida (Witek et al. 2009 and references therein). Sørensen et al. (2006) investigated relationships within the Gnathostomulida.

(Brusca and Brusca 2003; Sørensen and Sterrer 2009 and references therein; Margulis and Chapman 2010)