In this study, we used a recently developed supertrees method to test for shared phylogeographical signal in partially overlapping geographical ranges of lizards of the genus Liolaemus from the Andean Range in south-central Chile. We reconstruct mtDNA gene trees for three partially codistributed species (Liolaemus tenuis, L. lemniscatus and L. pictus), and our sampling effort is sufficient to allow statistical tests of shared signal between the combinations L. tenuis–L. pictus, and L. tenuis–L. lemniscatus. For both combinations, standardized maximum agreement subtrees scores showed statistically significant signal for shared pattern in regions of overlap, as evaluated by randomization tests (P < 0.001 and < 0.05, respectively). The matrix representation with parsimony tree obtained from the combination of the three different gene trees revealed concordant phylogeographical associations of all species, and was consistent with the geographical association of intraspecific haploclades with three Chilean bioclimatic zones. A multidimensional scaling analysis of several climate variables showed highly significant differences among these zones, which further suggests that they may have contributed to similar patterns of intraspecific divergence across all three species. In the mesomorphic zone in Central Chile, the species L. tenuis and L. lemniscatus may have codiverged in response to shared orogenic vicariant events, which likely predominated over climatic events associated with cycles of glacial advance and retreat. In the hygromorphic zone in southern Chile, however, glacial cycles likely predominated in structuring the phylogeographical histories of L. tenuis and L. pictus, although important ecological differences between these two caution against broad generalizations at this point.