The phylogeny of Nemertodermatida, a group of microscopic marine worms, was analysed using nucleotide sequences from the ribosomal LSU and SSU genes and the protein coding Histone 3 gene. All currently known species except Ascoparia neglecta and A. secunda were included in the study in addition to several yet undescribed species. Ascopariidae and Nemertodermatidae, are retrieved as separate clades, although not in all analyses as sister groups. Non-monophyly of Nemertodermatida was rejected by the Approximately Unbiased test. Nucleotide sequences deposited in Genbank before 2013 as nemertodermatid were validated against our dataset; some of them are shown to be chimeric implying falsification of prior hypotheses about nemertodermatid phylogeny: other sequences should be assigned new names. We also show that the genus Nemertoderma needs revision.