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The lizard genus Liolaemus is endemic to temperate South America and includes 190 species. Liolaemus bibronii has a large geographic distribution and inhabits a great diversity of habitats, including the Monte, Steppe, and high Andean grassland environments. Liolaemus gracilis has a similar body size and shape to L. bibronii; the two are parapatrically distributed, and L. gracilis is also widely distributed. Here we use the mtDNA cytb sequence data of these two species to investigate lizard phylogeographic patterns in southern South America. L. bibronii is paraphyletic with respect to L. gracilis, Liolaemus ramirezae, Liolaemus robertmertensi and Liolaemus saxatilis; it is composed of many genetically different allopatric haploclades, some of which are reciprocally monophyletic. We also found evidence for introgression between L. bibronii and L. gracilis in the same area that introgression was hypothesized in the Liolaemus darwinii complex. We discuss the distribution of the major haploclades with inferences of their population histories, the concordance of these clades’ distributions and histories with other lizard complexes studied with the same markers and methods, and taxonomic implications of these results.