The model organism Hydra belongs to the hydrozoan clade Aplanulata. Despite being a popular model system for development, little is known about the phylogenetic placement of this taxon or the relationships of its closest relatives. Previous studies have been conflicting regarding sister group relationships and have been unable to resolve deep nodes within the clade. In addition, there are several putative Aplanulata taxa that have never been sampled for molecular data or analyzed using multiple markers. Here, we combine the fast-evolving cytochrome oxidase 1 (CO1) mitochondrial marker with mitochondrial 16S, nuclear small ribosomal subunit (18S, SSU) and large ribosomal subunit (28S, LSU) sequences to examine relationships within the clade Aplanulata. We further discuss the relative contribution of four different molecular markers to resolving phylogenetic relationships within Aplanulata. Lastly, we report morphological synapomorphies for some of the major Aplanulata genera and families, and suggest new taxonomic classifications for two species of Aplanulata, Fukaurahydra anthoformis and Corymorpha intermedia, based on a preponderance of molecular and morphological data that justify the designation of these species to different genera.
