The goal of our work was to understand the role of a novel thermal environment in shaping the phenotypic expression of thermogenic capacity and organ size. To examine this we compared two populations of the South American rodent Phyllotis darwini from different altitudes (Andean and valley populations), taking advantage of the fact that this genus originated at high altitude in the Andean plateau. DNA mitochondrial analysis showed that the two populations were separated and then experienced different thermal regimens for at least the last 450,000 yr. We expected the two populations of P. darwini to present more metabolic and organ size similarities if phylogenetic inertia had been an important factor. In this sense, phylogenetic inertia means that the valley population would retain evolutionary adaptations of high altitude: a greater phenotypic flexibility in both physiological and morphological traits. In general, our results indicate that the actual thermogenic capacities (magnitude and flexibility) of the valley population are a consequence of phylogenetic inertia. On the other hand, results for organ size (magnitude and flexibility) could suggest that this population would have adapted to the less seasonal central valley.