In recent years, great attention has been devoted to the discovery and description of cryptic species, especially using DNA markers and new statistical approaches. Genetic data are useful for discovering new lineages that can then be treated as hypotheses to be tested using morphology. Here, we use multilocus genetic data and a thorough sampling to delimit species within the Greek legless skink. Phylogenetic analyses reveal high levels of genetic diversity, suggesting that Ophiomorus punctatissimus includes at least two species, East and West of the Aegean Sea. Moreover, species delimitation methods support at least two and up to five species within the western O. punctatissimus, and this result is shared among single-locus (ABGD, PTP, and GMYC) and multilocus coalescent (BPP) methods. We examined whether the two allopatric lineages exhibit morphological differentiation, but the different preservation methods used for the examined material led to inconclusive results. However, morphological conservatism in this semi-fossorial limbless skink possibly also played a key role. Finally, we formally recognize the East Aegean taxon as a separate species and we provide a differential diagnosis based on DNA diagnostic characters.