The spiny butterfly ray Gymnura altavela (Linnaeus 1758) is classified as Endangered by the International Union for Nature Conservation (IUCN) and considered Critically Endangered in the Mediterranean Sea and South-west Atlantic. Despite its status, few studies on the population biology and genetics for the species are available, undermining conservation efforts. In the present study, we evaluated the taxonomic status of Gymnura altavela along both sides of the Atlantic using COI sequences. Our genetic data support the existence of two genetically differentiated G. altavela lineages (West and East Atlantic) and further studies are required to evaluate the hypothesis that these lineages could, in fact, be cryptic species within this endangered batoid's genus.