Molecular phylogenetic analyses were conducted on species of some common tanaidacean families within the suborders Apseudomorpha and Tanaidomorpha based on partial DNA sequences for three genes: one mitochondrial (COI) and two nuclear (H3 and 28S). One nuclear gene (28S) resolved the two suborders as monophyletic groups while H3 and COI could only resolve Tanaidomorpha as monophyletic. The total evidence analysis (in-group taxa having at least two out of the three sequences) resolved both suborders as monophyletic, but only Tanaidomorpha showed strong support. All analyses support the monophyly of Kalliapseudidae (two out of three subfamilies represented) with the family clearly separated from the other apseudomorph families represented here. Relationships between and within the other apseudomorph families could not be resolved with strong support. Within Tanaidomorpha, most analyses supported a sister group relationship between the Tanaoidea (Tanaidae) and the Paratanaoidea. Results suggested that the monotypic Hargeria should be considered a junior synonym of Leptochelia, corroborating morphological evidence. Lack of resolution is likely due to inadequate taxon sampling, and differences in topology are largely due to weak support for relationships. This is the first attempt at using molecular data to determine phylogenetic relationships of tanaidaceans.