Liolaemus chiliensis, a widely distributed species in Chile, is unique in vertebrates because it presents populations with diploid (2n), triploid (3n) and mosaic (2n/3n) females, and with diploid and mosaic males whose meiosis produces reduced (n) and unreduced (2n) euploid gametes. With the aim of evaluating evolutionary consequences of polyploidy, we analyzed the morphological variability of 103 adults of L. chiliensis from separated geographic areas using both traditional and geometric morphometry in order to visualize shape and size differences in individuals with different ploidy. The results indicated that Liolaemus chiliensis is morphologically variable; a significant effect was observed for the interaction term of the three factors tested: sex, ploidy and locality. From the analysis, females exhibited higher values of axilla groin distance than males. There were also morphological differences in mosaic and triploid organisms with respect to the sympatric and allopatric diploids in the dorsal shape of the head, and the presence of intermediate phenotypes of triploids and mosaic lizards with sympatric males and females associated with the axilla groin distance. Results showed that there are morphological differences between polyploid and diploid organisms with both traditional and geometric approaches, suggesting evolutionary trend to differentiation; future research is needed to assess the underlying ecological and genetic mechanisms related to this phenomenon.