Rays and sharks are increasingly at risk of extinction due to anthropogenic pressures, including industrial fishing, bycatch and habitat degradation, and climate change. Their slow life histories and challenges in accurate species identification further hinder effective conservation. This study focused on ray and shark species along the coast of Côte d’Ivoire, aiming to achieve more accurate taxonomic resolution to improve specimen identification. To achieve this, we employed an integrative taxonomic approach combining morphological analyses and genetic data from two mitochondrial markers: COI (cytochrome c oxidase subunit I) and NADH2 (NADH dehydrogenase subunit 2), in order to describe the diversity of elasmobranchs landed, identify potential species complexes requiring further investigation, and assess the vulnerability of the captured elasmobranchs. Our study included 220 specimens of rays and sharks collected from 11 landing sites between February 2022 and September 2024. Sequence analysis revealed 32 Barcode Index Numbers (BINs), 11 of which were newly recorded in the Barcode of Life Data System (BOLD). Several unidentified genetic lineages were detected, suggesting the presence of cryptic species, misidentified taxa or potential undescribed species, including Torpedo cf. torpedo, Aetomylaeus cf. bovinus, Gymnura cf. sereti, Raja cf. miraletus, and Squalus cf. blainville. Notably, most of the identified species are listed as threatened on the IUCN Red List. These findings underscore the urgent need for comprehensive taxonomic evaluations and reassessments of conservation statuses, while also highlighting the importance of incorporating molecular tools into national fisheries monitoring and management strategies.