The type genus of Serpulidae, Serpula, along with closely related genera Crucigera and Hydroides account for approximately one third of all described species in the family. Although previous morphological and molecular studies unequivocally indicate that these three genera constitute a monophyletic group, the status of each genus remains unknown. In this study, the relationships among and within the genera Serpula, Crucigera, and Hydroides were investigated using maximum parsimony and Bayesian analyses of nuclear (18S and 28S rDNA) and mitochondrial (cytochrome b) genomic molecular markers plus morphology. The phylogeny supports the monophyly of Hydroides; however, Serpula forms a paraphyletic basal grade and Crucigera is polyphyletic. The lack of close relationship between Hydroides and Crucigera indicates that their similar opercular features are not homologous.