Anatolian mountains have played an important role in speciation and definition of biogeographical subregions and have been defined as “hotspots” of biodiversity. Because of its position and its long palaeogeographic and palaeoclimatic history, Anatolia acted in the past as a bridge or as a barrier for species' dispersal, providing natural pathways or acting as a vicariant agent, respectively. In this study we investigated the phylogeny and biogeography of a small fossorial snake, Typhlops vermicularis, in Anatolia, using formalin-preserved specimens and following a special protocol. We inferred phylogenetic relationships using partial 12S and ND2 sequences, and estimated divergence times of major lineages. Our mtDNA analysis revealed a hidden genetic diversity within Anatolian T. vermicularis. Four well-supported lineages occur within our sampled populations corresponding to respective refugia, which represent humid areas with dense forest vegetation in high altitude. The remaining populations, from the western and southeastern Anatolia, are almost genetically identical, representing a recent geographic expansion. A distributional disruption and a following allopatric fragmentation for T. vermicularis possibly resulted from climatic oscillations that occurred during the Miocene and Pliocene. We propose that extreme and sudden aridification led to distribution shrinkage of T. vermicularis, with genetic lineages surviving in refugia.