The Mediterranean morid codling Lepidion lepidion is thought to be endemic, yet its taxonomic distinctiveness from the morphologically similar and more wide-ranging Atlantic Lepidion eques is unresolved, and has been controversial since the beginning of the twentieth century. Despite the abundant taxonomic literature questioning the interspecific relationship between these taxa, their current status remains unchanged. To elucidate the differentiation of the specimens identified as L. lepidion and L. eques collected across much of their geographic ranges, the sequence divergence of the cytochrome oxidase I “DNA barcode” gene of the mitochondrial genome was evaluated. A network analysis indicates that the most observed haplotypes are common to both species throughout their Mediterranean and North Atlantic distribution areas. This molecular evidence suggests the absence of biogeographical barriers and is insufficient to support the different species designations, giving L. eques the taxonomic status of junior synonym of L. lepidion.