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Orbiniidae is a diverse group of annelids, comprising more than 200 described species grouped into 20 genera. Orbiniids are common and abundant in shelf habitats, representing nutritional resources for many types of sealife (including commercial seafood), and are subjects of ecological monitoring investigations,including as indicators of marine pollution. Despite their common appearance in benthic studies, orbiniids are one of the annelid families with an unresolved phylogeny and unclear diagnoses of most genera. Significant incongruence remains between traditional taxonomy and molecular studies in Orbiniidae, with the genera Scoloplos, Leitoscoloplos, Leodamas, Orbinia, Naineris and Phylo recovered as paraphyletic in several molecular studies, but still considered as valid in current monographs. Here, we present our attempt to revise the phylogenetic system of Orbiniidae using genome skimming data generated by the Illumina sequencing technology. We successfully obtained whole-genome reads for 96 orbiniid specimens from 10 different genera and 55 species. The chosen target genes included 13 mitochondrial protein coding, 2 mitochondrial ribosomal, and 4 nuclear ribosomal markers. Maximum Likelihood and Bayesian analyses of the supermatrix resulted in a robust orbiniid phylogeny showing six major clades. Clade 1 combined the representatives of Scoloplos and Leitoscoloplos. Clade 2 consisted of specimens belonging to Orbinia and Phylo, together with Methanoaricia dendrobranchiata. Clade 3 included all the Leodamas species. Clade 4, with a single species of Orbiniella represented by two specimens, was of uncertain placement due to a possible long branch attraction artifact. Finally, Naineris was shown to be polyphyletic, with N. quadricuspida (type species of the genus) as clade 5 being recovered separately from the rest of the species, which together with Protoaricia formed clade 6. We discuss the topologies of the obtained trees and propose changes for the current phylogenetic system of Orbiniidae.