Abstract:[Background] In May 2016, an unprecedented outbreak of nodulous esophagitis occurred among the captive juvenile Siamese crocodiles (Crocodylus siamensis) in Xiamen Lonsun crocodile zoo, and diseased crocodiles manifested anorexia and some of them even died. [Objective] Pathogenic identification of crocodiles’ pathological materials was performed to explore its causes, to provide data for estimating this disease, and to make references for preventive treatment. [Methods] The bacteria isolated from crocodiles’ foci were identified by the physiological and biochemical characteristics, 16S rRNA gene sequence analysis, artificial infection test and sensitive drug test. [Results] Three bacterial strains isolated from esophagus, liver, and blood of diseased crocodiles, were identified as Proteus penneri by means of morphological, physiological and biochemical characteristics, and 16S rRNA gene sequence analysis. Besides, the P. penneri strain 2202 was confirmed as pathogen causing morbidity and mortality in C. siamensis after artificial infection test. The susceptibility test showed that the resistance rates of 3 isolated strains to 12 antimicrobial agents were all equal to 33%. The 3 pathogens were sensitive to 7 medicines, including enrofloxacin, sulfamethoxazole, cefotaxime, kanamycin, tetracycline, doxycycline, and nalidixic acid; resistant to rifampicin, penicillin G, erythromycin, and chloramphenicol; and intermediate resistant to streptomycin. [Conclusion] As a result, P. penneri was directly related to the death of diseased C. siamensis. To the best of our knowledge, this is the first report about P. penneri, the opportunistic pathogen mostly affected human, infected the captive crocodilians.