We used ecological niche modelling projected as species' potential (based on the original vegetation map) and extant (based on the 2000 land use and vegetation map) distributions to analyse changes on patterns of endemism of terrestrial mammals occurring in Mexico. Based on the biogeographic method of Parsimony Analysis of Endemicity, we obtained cladograms under scenarios of species' potential distribution (t1) and extant distributions (t2). We found that the resolution of consensus cladogram

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... n t2 was poorer, while there were more geographic synapomorphies in t1, and more autapomorphies in t2 due to a reduction of species' distributions as a consequence of deforestation. We defined a hierarchical regionalization with two regions with the cladogram of t1; a transitional zone, two subregions, five dominions, and 15 provinces. Conversely, the consensus cladogram of t2 had a basal trichotomy, and the position of the Sierra Madre Occidental changed compared with t1. In t1 and t2, the Yucatán Peninsula+Chiapas+Isthmus of Tehuantepec clade was maintained, although in t2 it was separated from the remaining areas of the country. The impact of deforestation on species distributions strongly affected the biogeographic regionalization of terrestrial mammals in Mexico.