In the present study, the taxonomic status of Microlophus heterolepis and M. yanezi is reviewed. Although M. heterolepis is one of the identified species present in Chile, incongruity about their geographical distribution, habitat and ecological characteristics are evident, so its true determination is an issue. Type materials and original descriptions of M. heterolepis were compared with its closest species M. yanezi, and morphological (scaling, lineal morphometric and geometric morphometric) and molecular analysis (cytb) were performed. The results show that: 1) M. heterolepis was originally described for the locality of Tacna in Peru, 2) morphological descriptions by Donoso-Barros (1966) correspond to a lizard in the desert, but their ecological characteristics were described erroneously as a kind of rocky intertidal, and 3) there is agreement with previous authors that both species are valid. However, based on our results, the geographical distribution of M. heterolepis is restricted to Peru, while M. yanezi is a validly described species from Chile.