The lacertid wall lizards of the genus Podarcis (Wagler, 1830) originate from Western Europe and are divided into 24-25 species (Speybroeck et al., 2020). Despite the abundance of phylogenetic studies referring to the genus, the relationships among certain species, as well as the taxonomic status of some genealogical lineages, remain unclear due to great genetic diversity. The common wall lizard Podarcis muralis has a relatively wide distribution and despite the existence of various molecular studies focused on this species, its Greek populations had never been thoroughly sampled until now. To fill in this geographical gap, we sampled the species’ Greek distribution and constructed phylogenies that uncovered the presence of at least five monophyletic lineages that correspond to different geographic regions. Furthermore, species delimitation analyses assigned all lineages to a single species diversifying during the early Pleistocene (c. 1.93 mya). The strong association of the genetic lineages with specific geographical regions coupled with the Pleistocene diversification of the group imply the presence of multiple refugia within Greece and, by extension, the Balkan peninsula, supporting a refugia-within-refugia scenario. Finally, in an effort to clarify the position of these new samples within the larger phylogeny of P. muralis, a larger phylogeny was constructed which indicated that the Greek populations cluster with the central European, Italian and Turkish populations of the species.