Archaeolacerta bedriagae is a rock-dwelling lizard endemic to the Corso-Sardinian insular system. We investigated the phylogeography of the species by using the mitochondrial ND4 and flanking tRNAs genes from 94 specimens belonging to 19 populations. Phylogenetic, Barrier, and SAMOVA analyses revealed a highly structured pattern characterized by two levels of discontinuities in the geographical distribution of mtDNA diversity: (i) a deep phylogeographic break in Northern Corsica between Lineage A, restricted to northernmost Corsica, and Lineage B widespread all over the remaining range of the species, and (ii) some minor phylogeographic discontinuities within lineage B, which is sub-structured into six closely related haplotype clades with remarkable concordance with geography. The first evolutionary event concerning the split between the two main lineages from an ancestral population occurred in the Upper Pliocene (5.87-3.68 mya), while the divergence within lineage B would have started from the Upper Pleistocene (2.5-1.6 mya), between Corsican and Sardinian populations. Somewhat later (1.7-1.1 mya), the Sardinian ancestral population underwent fragmentation into population groups inhabiting North, Central, and South Sardinia. As inferred from previous allozyme surveys, the divergence among population groups would be driven by allopatric fragmentation, while the discrepancy concerning the major partition into two lineages inferred from mtDNA but not apparent in analysis of allozymes needs further investigation.