The phylogeny of scale-worms, benthic polychaetes carrying dorsal scales (elytra), including taxa from Acoetidae, Aphroditidae, Eulepethidae, Pholoidae, Pholoididae, Polynoidae and Sigalionidae (Aphroditiformia), is assessed from the nuclear markers 18SrRNA and 28SrRNA, and mitochondrial 16SrRNA and cytochrome c oxidase subunit I (COI), and 24 morphological characters. The data sets are analyzed both separately and combined, with Bayesian analyses, maximum likelihood and parsimony. In total, 56 terminal taxa are examined, including 48 taxa from all scale-worm families, and eight out-group species. The results indicate that Aphroditidae and Eulepethidae are the most basally placed families among the scale-worms. The Pholoididae and Pisionidae are positioned within and synonymized with the Sigalionidae, and Pholoidae may be part of the same group. The subfamily Iphioninae falls out as sister group to a clade consisting of Polynoidae and Acoetidae and is elevated to Iphionidae. The families now included in the Aphroditiformia are Acoetidae, Aphroditidae, Eulepethidae, Pholoidae, Polynoidae, Iphionidae and Sigalionidae, and the subfamily name Harmothoinae and Acholoinae are treated as a junior synonyms of Polynoinae.