This paper presents an isotopic characterization (δ13C and δ15N) of modern huemul from Patagonian Andean forest. This deer is considered an endemic species, now inhabiting the sub‐Antarctic forest of Chile and Argentina. We analyse if the isotopic signals of the modern huemuls can be used as geographic markers on two distinct spatial scales. Firstly, on the intra‐forest level, we analyse the relation between the δ13C and δ15N of the huemul and the annual precipitation in the place in which the sample was collected. Secondly, on the inter‐environmental level, we evaluate to what extent the huemul's isotopic signal differs from that of the guanaco (Lama guanicoe), an herbivore that occupies Patagonia's continental steppe. The results reveal that, on the one hand, there is no relation between the isotopic values of modern huemules and precipitation levels, whereas on the other hand, the modern huemul is different from the guanaco in both isotopes. We believe that this difference between the herbivores is associated with the isotopic signals at the base trophic chain, which is influenced by the precipitation gradient. In this way, even though for now, these isotopic markers turn out not to be useful for differentiating between huemuls coming from sectors of the forest with marked differences in precipitation, it is possible to distinguish herbivores coming from the forest and steppe of continental Patagonia, enabling the use of δ13C and δ15N as geographic markers. The isotopic characterization of δ13C and δ15N of the modern huemuls and its relation to the Patagonian Andean forest has strong implications for paleoecological and archaeological aspects of this environment, including the biogeographical history of the huemul, and in order to the test the models of use and exploitation of the forest by hunter‐gatherers in the past. Copyright © 2013 John Wiley & Sons, Ltd.