Retortamonads (Retortamonadida; genera Chilomastix and Retortamonas) are a small group of protists comprising intestinal commensals of both vertebrates and invertebrates and one free-living species of the genus Chilomastix. Molecular phylogenetic studies showed that retortamonads are closely related to diplomonads, Carpediemonas, Dysnectes, Hicanonectes, Kipferlia and two undescribed lineages of free-living Carpediemonas-like organisms, together forming the monophyletic excavate group Fornicata. For a long time Retortamonadida have been assumed to be a monophyletic group. However, first molecular phylogenetic study including sequence data from both Retortamonas and Chilomastix suggested that Retortamonadida are paraphyletic and that diplomonads branch within Retortamonadida. Retortamonads still remain poorly studied protist group and their phylogeny is unclear. We sequenced and analysed SSU rDNA of ten Retortamonas and four Chilomastix SSU rDNA sequences. In addition, we sequenced SSU rDNA of an undescribed enteromonad lineage. The phylogenetic tree of Fornicata was largely unresolved and the phylogenetic position of the genus Chilomastix remained unclear. On the other hand, the genus Retortamonas and diplomonads formed a robust clade. Retortamonas sequences split into three host-specific lineages. The...