Aphroditiformia represents one of the most successful radiations of annelids, and is therefore an interesting model to understand morphological and functional evolution. Previous phylogenetic analyses yielded most families as monophyletic but excluded anchialine and interstitial species while failing to recover relationships within Sigalionidae. Here we address these shortcomings through the analysis of four molecular markers and 87 morphological characters sampled across 127 species under the assumptions of parsimony and model-based methods. Of the 34 newly sequenced taxa, five anchialine and 24 interstitial species were included, with increased representation of Sigalionidae. An additional 28 elusive Sigalionidae taxa were included, represented only by morphological partitions. Molecular and morphological partitions were evaluated under exhaustive sensitivity analyses, testing the effects of alignment algorithms and optimization criteria on tree topologies. Our trees congruently recovered six clades corresponding to the families within Aphroditiformia: Acoetidae, Aphroditidae, Eulepethidae, Iphionidae, Polynoidae and Sigalionidae, respectively. An anchialine polynoid lineage was nested among strictly deep sea species, and interstitial pisionids and pholoids formed two independent clades nested within Sigalionidae. Additionally, Sigalionidae resulted in four clades, defined by combinations of apomorphies, and hereby we propose the subfamilies Pelogeniinae, Pholoinae, Pisioninae, Sthenelanellinae, as well as the provisionally included polyphyletic Sigalioninae.