Currently, the genus Zenopsis, also known as silver John Dory, comprises at least five valid species with a wide range of distribution. However, recent studies have proposed the existence of a new Zenopsis species inhabiting the Indian Ocean, and a preliminary search in the Barcode of Life Database reveals the presence of different barcode index numbers (BIN) for the nominal species Zenopsis conchifer. In the Southwest Atlantic Ocean (SWA), Z. conchifer is the only species reported so far. Therefore, the aim of this work was to evaluate, at the molecular level, the potential taxonomic diversity within the genus Zenopsis and to assess if the species occurring in the SWA corresponds with Z. conchifer. Using data available in worldwide genetic databases, a maximum likelihood tree, a BIN, and an automatic barcode gap discovery analysis were carried out. Additionally, specimens sampled from the SWA were morphologically compared with specimens from different parts of its distribution using available data. The specific identity at the molecular level of specimens occurring in the SWA was confirmed as Z. conchifer. The results of the molecular analysis highlight the existence of hidden specific diversity within the genus.

The skate fauna in the Southwest Atlantic Ocean (SWA; 34–55° S) is represented by ~32 species, many of which share external features that have led to misidentifications and deficient fishery statistics. The use of DNA barcoding to discriminate SWA skate species was explored after 20 years of surveys. COI sequences were subjected to distance-based neighbor-joining (NJ), maximum likelihood (ML), barcode index number (BIN), automatic barcode gap discovery (ABGD), and nucleotide diagnostic character (NDC) analyses. For widely distributed species, a haplotype network was built. Overall, 187 specimens and 31 egg cases from 26 skate species were barcoded. NJ and ML analyses showed that nearly all species exhibited unique barcodes or clusters of closely related haplotypes, except for Psammobatis normani/P. rudis and Dipturus trachyderma/D. argentinensis. The first pair was discriminated by NCD. BIN analysis recovered 17 groups, whereas ABGD recovered 23, better reflecting taxonomic diversity. In summary, 24 species were resolved by COI. Phylogeographic signals were observed for Amblyraja doellojuradoi and Zearaja brevicaudata. Compiling our results with data from BOLD, almost all the species occurring in the area possess barcodes, contributing to completing and curating the BOLD reference library, which constitutes an important tool for resolving taxonomic issues, tracing fishery products, and performing eDNA biomonitoring.