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Aim Our aim was to determine the combined impacts of Pleistocene climatic oscillations and glacial periods with recognized biogeographical barriers on the evolutionary history of huemul deer ( Hippocamelus bisulcus). Location Southern Chile and Argentina's Andean forest, and Patagonian fjords. Methods We examined the phylogeography of huemul using 772 bp of the mitochondrial DNA control region sequence from 275 samples (29 locations) collected throughout the distributional range of the species. We grouped samples into clusters based on Bayesian genetic and spatial structure analyses and reconstructed the species' phylogeographical and demographic history. Results We observed 63 haplotypes that grouped into three clusters (Central Chile, North Patagonia and South Patagonia). All but five haplotypes in North and South Patagonia were distributed locally. Bayesian skyline plots showed that population sizes remained fairly constant until an increase during and after the Last Glacial Maximum. Genetic diversity was generally low, except in three populations in the eastern Andes and on Wellington Island (Patagonian fjords). Main conclusions Our results suggest that the biogeographical separation of huemul into phylogeographical groups has been heavily influenced by Pleistocene glacial stages, and more recently by habitat fragmentation and isolation. This provides the first evidence that the region west of the Cordilleran ice field was a refugium for at least one species of large mammal during the Pleistocene in southern South America. These results have direct implications for the conservation and management of this endangered deer species. [ABSTRACT FROM AUTHOR]