Abstract: The Chinese alligator (Alligator sinensis) is a critically endangered species in China. Wild populations of Chinese alligator are on the edge of extinction. Through a release program, some captive-bred alligators will be selected and released into the wild to supplement and renew natural populations. The purpose of this study was to provide data to select healthy individuals for release. Through bacteriological and molecular identification, six different genera, eight species and an unclassified bacterium were identified in 13 bacterial strains, which were isolated from the cloaca of 25 Chinese alligators. One genus and four species were identified in eight bacterial strains, which were isolated from the water where the alligators live. According to the analysis, except for the unclassified bacterium, the other bacteria from the cloaca were not pathogenic and were different from the bacteria isolated from the water. Thus, it was concluded that the 24 Chinese alligators were healthy, and could be selected to be released into the wild. As subject AS12 was identified carrying an unclassified bacteria, of which the characteristics were unknown, it was suggested that the AS12 individual not be released.