After sudden death with a history of about two weeks ruminal tympany, a 3-year-old, male alpaca from Huantaiqi Zoo, Chongqing, China was presented to the Animal Diseases Rapid Diagnosis Center, Southwest University, Chongqing, China for diagnosis of the death causes. At necropsy, the primary pathological lesions were found in the lung. A pronounced hemorrhage with topical congestion and lobular pneumonia was identified. Sero-fibrinogenous pleural effusion was also detected in the thoracic cavity. After necropsy, the lung sample was processed for histological examination, while lung, hydropericardium, and heart-blood samples were processed for bacteriological examination. From the lung tissue, abundant fluid exudate was found in the pulmonary alveoli. Meanwhile, a mild to moderate hemorrhage and inflammatory cells infiltrations were also observed in the lung sections. Pure isolates on the 5.00% defibrinated sheep blood agar were submitted for identification by morphological and molecular methods. Sequencing results indicated that the Gram-negative sporadic bacilli were all belonged to Morganella morganii. To the best of our knowledge, this is the first record of M. morganii induced pneumonia in an alpaca.