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Aim To understand how the activity budgets of ectotherms vary in mountain areas with high microclimatic and habitat heterogeneity, and how these factors together with habitat modulate the assemblage of ectotherm communities. Location Tajzara Basin, Cordillera de Sama (3,600-4,300 m a.s.l.), Department of Tarija, Bolivia. Taxon Four lizard species of the genus Liolaemus. Methods After parameterizing the thermal physiology of each species and recording operative temperature time series with dataloggers, we calculated activity budgets for every species across 30 sampling sites. By multimodel inference we evaluated how activity budgets varied across the topography. We also assessed how abundances of each species were predicted by activity budgets, restriction time, temperature deviation, habitat covers and exposure to cold microclimate. Results Activity budgets were not only influenced by elevation but also by the exposure to cold air that comes through saddles from the eastern side of the mountain divide. Although thermal physiological parameters were relatively similar among the species, their abundances were conditioned to different extents by activity budgets, habitat and microclimates. Main conclusions The abundance and distribution of each species across these lizard communities reflect the microclimatic heterogeneity originated by complex topography, which uncouples activity budgets from elevation. Only one species was confined to cold microclimate refugia with higher exposure to Fohn effect. Despite having a relatively similar thermal aspect of fundamental niches, lizards may differ in their realized niches by habitat selection. Habitat specialization could compromise the persistence of some species under global warming by reducing the dispersal possibilities to certain areas where population sustainability might be impaired in the long term. Understanding the heterogeneity of microclimates and habitats and the physiology of the species partially explains their distribution at local scale, and provides insights on how to best confront upcoming climate change effects.