With a global population estimated at 2000 individuals between Argentina and Chile, less than 1% of its historical population, the huemul (Hippocamelus bisulcus) is categorized as "Endangered". Through a population viability analysis, we sought to estimate the viability of two huemul populations under different threat scenarios. Through a sensitivity analysis, we expected to identify those threats, and environmental or population variables that are more relevant for each population survival. Our main goal is to contribute to the management of the species in Chile through threats prioritization seeking to focus future conservation strategies. This research involved huemul populations from the Nevados de Chillan-Laguna del Laja Biological Corridor Biosphere Reserve (NCLL) and the Cerro Castillo National Park (PNCC). The NCLL population showed a very low probability of survival with a mean time to extinction of 45.9 years; in contrast, PNCC population exhibited a higher probability of survival with a mean time to extinction of 68.6 years. Predation and harassment by dogs seem to have the most significant negative impact on both populations' fate. Additionally, populations were highly sensitive to the percentage of reproductive females and female mortality. Based on our findings, we proposed concentrating conservation efforts on reducing or eliminating dogs' chances to attacks and predate huemul, as well as to focus surveillance actions on females.