New sequences of the partial rDNA gene coding for the mitochondrial large ribosomal subunit, 16S, are derived from 47 diverse hydrozoan species and used to investigate phylogenetic relationships among families of the group Capitata and among species of the capitate family Corynidae. Our analyses identify a well-supported clade, herein named Aplanulata, of capitate hydrozoans that are united by the synapomorphy of undergoing direct development without the ciliated planula stage that is typical of cnidarians. Aplanulata includes the important model organisms of the group Hydridae, as well as species of Candelabridae, Corymorphidae, and Tubulariidae. The hypothesis that Hydridae is closely related to brackish water species of Moerisiidae is strongly controverted by 16S rDNA data, as has been shown for nuclear 18S rDNA data. The consistent phylogenetic signal derived front 16S and 18S data suggest that both markers would be useful for broad-scale multimarker analyses of hydrozoan relationships. Corynidae is revealed as paraphyletic with respect to Polyorchidae, a group for which information about the hydroid stage is lacking. Bicorona, which has been classified both within and outside of Corynidae, is shown to have a close relationship with all but one sampled species of Coryne. The corynid genera Coryne, Dipurena, and Sarsia are not revealed as monophyletic, further calling into question the morphological criteria used to classify them. The attached gonophores of the corynid species Sarsia lovenii are confirmed as being derived from an ancestral state of liberated medusae. Our results indicate that the 16S rDNA market could be useful for a DNA-based identification system for Cnidaria, for which it has been shown that the commonly used cytochrome c oxidase subunit 1 gene does not work.