The oegopsid squid family Onychoteuthidae was recently revised based on morphology, but sufficient material for a complementary molecular analysis has not been available until now. In the present study, over 250 sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA for 222 individuals were analysed to create a combined phylogeny for the family. Results support monophyly for the family and all seven onychoteuthid genera (including Moroteuthopsis, established herein as the senior genus name for species formerly attributed to Kondakovia); 29 genetically distinct species were recovered, with the BIN (Barcode Index Number) analysis for COI showing good congruence overall with morphological species groupings. No sequences were available for five additional known species, making the total family diversity likely to exceed 34 species. Seven of the BINs formed in this study appear to represent undescribed taxa, suggesting that even in this relatively well-studied family, much additional work remains before a comprehensive understanding of the diversity and evolutionary relationships for the Onychoteuthidae can be achieved.