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Habitat partitioning is considered one of the main mechanisms of coexistence among small mammals. This is especially evident in arid environments where resources are particularly scarce. Habitat characteristics such as vegetation heterogeneity and complexity are expected to increase species coexistence, increasing the number of microhabitats that can be occupied by species with different requirements. The Andean foothills can be considered as an ecotone between the Monte and Altoandina phytogeographic provinces as they harbor species from both. Consequently more species are thought to coexist in this area. The objectives of this study were to assess the macro- and microhabitat selection of the small mammal assemblage inhabiting the Andean foothills during wet and dry season and to determine how animals segregate environmental resources to ensure their coexistence. We found that habitat selection occurs at both scales in the Andean foothills. Two species, Eligmodontia moreni and Phyllotis xanthophygus, were capable of distinguishing among macrohabitat types, whereas all species showed habitat selection at the microhabitat scale. We registered selection during both seasons, with some overlap of resource selection during the wet season and the greatest segregation of microhabitat resources during the dry season. Therefore, this work evidence that the assembly of small mammals is sensitive to habitat structure especially in dry seasons where resources are constraints due to arid conditions of Andean foothills.