Cystic echinococcosis (CE) is a zoonotic parasitic disease associated with Echinococcus granulosus. The parasite is maintained by domestic and wild canids as definitive hosts with several ungulate species as intermediate hosts in domestic and peridomestic transmission cycles. In Chile, CE is endemic, and the role of livestock and dogs (Canis lupus familiaris) in the cycle and the accidental infection of humans are widely documented at rural sites. However, the role of wild herbivores in wild cycles or the potential transmission of CE from livestock is still unknown in Chile and the rest of South America. We used molecular techniques to describe CE infecting a Patagonian huemul (Hippocamelus bisulcus) in Cerro Castillo National Reserve (Aysén region, Chile). We make inferences about the risk of disease spillover from sympatric domestic and wild species. The DNA-based molecular analysis revealed that the huemul was infected with E. granulosus G1 genotype, sharing haplotypes with other G1 samples collected from sheep (Ovis aries) and cattle (Bos taurus) worldwide. Geographic overlap between sheep and huemul populations in the reserve likely facilitates parasite spillover into wild deer populations, with shepherd or stray dogs and wild foxes (Lycalopex culpaeus) potentially acting as bridging hosts between livestock and the endangered huemul. Further studies are warranted to understand the implications of E. granulosus for huemul conservation throughout the Chilean Patagonia.