Corynebacterium pseudotuberculosis is an intracellular bacteria and the etiologic agent of caseous lymphadenitis in domestic and wildlife species. We report C. pseudotuberculosis infection in Patagonian huemul (Hippocamelus bisulcus) from the Cerro Castillo National Reserve, Region of Aysen, Chile. Subcutaneous abscesses in the abdominal and pectoral regions from two animals were sampled and bacteriologic isolation was performed. In both cases, we isolated a C. pseudotuberculosis strain belonging to the ovine genotype. In addition, one isolate was resistant to ciprofloxacin and streptomycin. We report that H. bisulcus is a susceptible species to this bacterium, which is transmitted by direct or indirect contact with domestic sheep (Ovis aries) and which represents a potential conservation threat to populations of H. bisulcus. Additional research and prevention efforts should be addressed.