Sphaerodoridae is a small, morphologically well-defined group of annelids, with remarkable spherical tubercles covering their body surface. They have generally been considered as part of Phyllodocida, but there is no consensus about its sister group relationships. Monophyly and internal phylogenetic relationships have never been tested. We present the first phylogenetic analysis of the family, including 33 individuals of 19 species in five genera of Sphaerodoridae, and a wide representation of other Phyllodocida, based on molecular data from nuclear 18S rDNA (2240 bp), mitochondrial 16S rDNA (614 bp), and cytochrome c oxidase subunit I (657 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum parsimony, maximum likelihood and Bayesian inference. Results show maximum support for the monophyly of Sphaerodoridae, but sister group relationships remain unclear. The genera Sphaerodoropsis and Sphaerodoridium are found to be paraphyletic. Monophyly of Clavodorum, Ephesiella and Sphaerodorum could not be tested because only one species was included for each of these genera. At least six of the morphotypes included in the study do not fit within current species descriptions, suggesting undescribed species. Finally, the transfer of Sphaerodoropsis minuta back to Sphaerodoridium is proposed.