The Anomalodesmata Dall, 1899 includes some of the rarest and most specialised species of marine bivalves. This rarity has consequently constituted the greatest obstacle for understanding the internal relationships due to the low representativeness of species present in any phylogenetic reconstructions. Therefore, with the primary purpose of creating a more comprehensive morphological analysis, data including all the anomalodesmatan families were gathered into a cladistic analysis. Our data set includes, for the first-time, information about members of the families Clistoconchidae, Cetoconchidae, Protocuspidariidae, Spheniopsidae and the recently described Bentholyonsiidae. Information on shell morphology, anatomy and behaviour of anomalodesmatans was compiled through a review of the literature (from 1895 to 2022) and a re-analysis of shells and internal anatomy of some freshly collected and archived specimens in museum collections around the world. Our analysis suggests a deep division of the Anomalodesmata into two distinct clades: the first generally composed of shallow water species from 12 families and a second clade of a carnivorous lineage mainly comprising deep water species from 10 families. Consequently, a new topology for Anomalodesmata is suggested bringing new insights into the interfamilial relationships of this sometimes bizarre clade of bivalves.