On January 2020, an outbreak of acute mortality was detected in the capybara (Hydrochoerus hydrochaeris) population kept in the Cordoba Zoo Conservation Center (CZCC) in Spain. Morbidity and mortality rates were 71%, and the fatality rate was 100%. Macroscopic examination revealed multifocal nodular lesions with fibrinonecrotic exudate in lungs and mesenteric lymph nodes. Microscopic lesions were characterized as severe acute fibrinopurulent bronchopneumonia and generalized vascular changes. Cultures and biochemical analyses yielded Yersinia pseudotuberculosis (YPT). This species was confirmed by both PCR and MALDI-TOF. This report describes the first outbreak of fatal YPT infection in zoo animals in Spain and confirms that capybaras are highly susceptible to this pathogen, which could be of animal health, conservation, and public health concern. Future studies are warranted to determine potential sources of YTP infection in zoos to prevent future cases in susceptible species, including humans.