The Mediterranean Basin has been subjected to important geological and paleogeographic events that have shaped the evolution of the faunal assemblages that inhabit it. Two main events can be highlighted, the closure of its eastern margin by the Gomphotherium Land Bridge, and the temporal closure of the connection to the Atlantic Basin during the Messinian Salinity Crisis. These two events shaped the diversity of the chondrichthyan assemblages of the Mio–Pliocene Mediterranean, and their consequences can be observed even in the modern faunal composition. To better understand the taxonomic and ecological composition of the Mediterranean chondrichthyan faunas between the aforementioned events, and how they affected their evolutionary dynamics, we have performed a complete systematic and paleoenvironmental study of the chondrichthyan assemblage recovered from various Late Miocene localities at the municipality of Alcoy Basin (Alicante, eastern Spain). Our analysis allowed us to recognize up to 20 taxa of sharks and rays recovered from Miocene deposits. In addition, we reconstruct the paleobathymetry of the El Muro fossil site, based on the estimation of the Oceanization Index for foraminifera, as well as by the elasmobranch fossil assemblage via weighted bootstrap analysis. We expect that this first description and study of the Miocene chondrichthyan taxa from this area of eastern Spain could help us create a comparative framework to compare these communities with other areas, as well as show the changes in the elasmobranch species that have inhabited the Mediterranean Basin during and after the Messinian Salinity Crisis.