The Lophogastrida are primitive Mysidacea and comprise only six genera. One of these, Eucopia is considered as highly specialized and constitutes the family Eucopiidae; the other genera constitute the Lophogastridae. Among the latter family, the genus Gnathophausia is closely related to Eucopia, with two species (G. gracilis and E. sculpticauda) sharing similar morphological characteristics (i.e. ornamentation (spines) of the uropods, and the gastric mill). This indicates that these species are phylogenetically related. To test this hypothesis, the partial 16S mitochondrial ribosomal RNA gene from various representative species of Gnathophausia and Eucopia were compared. The resulting phylogenetic tree suggests that each genus is monophyletic, and that Gnathophausia, which is the deepest-branching genus, is the most primitive, with the Eucopiidae originating from the Lophogastridae. The molecular results support the morphological hypothesis, and suggest an early separation of the two genera or a rapid divergence of Eucopia due to morphological specialization.