Selection occurs when animals choose from among alternative habitat resources they find available in the environment. As selection is a hierarchical process, it can be studied at multiple spatial scales. Subterranean rodents are a good model to study habitat selection because of their low dispersal ability and easily identifiable perturbed areas. Using a comparative data from multiple distinct locations, we analyzed if Ctenomys mendocinus selects different habitat units at a macroscale and identify which variables most influence its activity at a microscale. We conducted this study in an extreme environment in terms of resource abundance and climatic conditions, generating interesting new insights into patterns of habitat selection by this species. We found that minimum soil depth and the abundance of Fabiana punensis shrub were the most important variables determining C. mendocinus activity at the microscale. Also, the changes in these variables may probably influence the selection of habitat units found at the macroscale.