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The Balkan Wall Lizards are divided in two phylogroups, the “Podarcis tauricus” and “P. erhardii” species complexes. Both include cryptic species that were recently discovered in maternal molecular phylogenies and have undergone taxonomical rearrangements. The central Aegean islands host two of these species, one from each phylogroup, that present completely allopatric geographic distributions; the endemic P. milensis is found on the Milos island-group, while almost all other Cycladic islands are home to P. erhardii. Velopoula, a small isolated islet, lies at the westernmost edge of the Milos island-group and for the past many decades has been considered part of the P. milensis distribution. In this study, we collected DNA sequence data from the lizards of Velopoula, to discover that they, in fact, belong to P. erhardii. We built an updated, time-calibrated mitochondrial phylogeny of P. erhardii, including specimens from the islet and unrepresented regions of the neighboring mainland, in order to evaluate the phylogenetic position of the Velopoula population and infer its origin and diversification history. According to our results, this population represents a highly divergent lineage that split at the Miocene/Pliocene boundary. This rejects the hypothesis of a recent colonization of Velopoula from another insular or mainland P. erhardii population and provides evidence for a new, relict taxon endemic to this islet. Through a thorough bibliographic search, we retrace the mistaken taxonomic assignment of the Velopoula Wall Lizards and discuss their assignment as a new potential species within the “P. erhardii” species complex.