Complete 18S rDNA sequences of two species of the Tantulocarida Arcticotantulus pertzovi (Basipodellidae) and Microdajus tchesunovi (Microdajidae) were obtained and used for estimating the relationship of the class with other Crustacea. This constitutes the first use of tantulocaridan gene sequences, and we conclude that the Tantulocarida are very close relatives of the class Thecostraca, which comprise cirripedes, ascothoracidans and the enigmatic facetotectans. With much lower confidence, the Tantulocarida are also indicated as nested within the Thecostraca, being sister group to the Cirripedia. We therefore discuss morphological similarities and differences between tantulocaridans and the thecostracans in search of potential synapomorphies, including a possible relation to the parasitic barnacles (Rhizocephala). We conclude that the cement gland of the tantulus larva and the cirripede cyprid might be homologous structures, but that similarities in host infection and root systems between the Tantulocarida and the Rhizocephala are, on present evidence, likely to be homoplasies evolved by convergent evolution into advanced parasitism. The precise position of the Tantulocarida in relation to or within the Thecostraca must be pursued by a more extensive database of genetic markers.