This study aims to analyze the thermal biology and climatic vulnerability of two closely related lizard species (Stenocercus festae and S. guentheri) inhabiting the Ecuadorian Andes at high altitudes. Four physiological parameters-body temperature (T b), preferred temperature (T pref), critical thermal maximum (CT max), and critical thermal minimum (CT min)-were evaluated to analyze the variation of thermophysiological traits among these populations that inhabit different environmental and altitudinal conditions. We also evaluate the availability of operative temperatures, warming tolerance, and thermal safety margin of each population to estimate their possible risks in the face of future raising temperatures. Similar to previous studies, our results suggest that some physiological traits (CT max and T b) are influenced by environmental heterogeneity, which brings changes on the thermoregulatory behavior. Other parameters (T pref and CT min), may be also influenced by phylogenetic constraints. Moreover, the fluctuating air temperature (T air) as well as the operative temperatures (T e) showed that these lizards exploit a variety of thermal microenvironments, which may facilitate behavioral thermoregulation. Warming tolerance and thermal safety margin analyses suggest that both species find thermal refugia and remain active without reducing their performance or undergoing thermal stress within their habitats. We suggest that studies on the thermal biology of tropical Andean lizards living at high altitudes are extremely important as these environments exhibit a unique diversity of microclimates, which consequently result on particular thermophysiological adaptations.