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The Yangtze finless porpoise(Neophocaena phocaenoides asiaeorientalis)is one of subspecies of the finless porpoise (Neophocaena phocaenoides), listed among the nation`s protected animals of the second order and categorized as the endangered species by the IUCN red list. This species distribute mainly from Changjiang (Yangtze) River, Dongting Lake, Poyang Lake and their branches in China. Though rearing of the Yangtze finless porpoise is successful, there are still many problems to be solved. Respiratory disease is the one of the problems in its rearing process. Furthermore, lack of accumulation of disease analysis and summarization, we rely heavily on our experience therapy at the aspect of respiratory disease, pathogen identification and drug selection are known rarely. In this study, we compared the difference of predominant flora incubating in the respiratory tract of the animals between that in natural environment and that in captivity for the purpose of guidance of disease monitoring, prevention and treatment.Expiratory samples and nasal swab samples of eight healthy animals habitated in Tian-e-zhou natural reserve were taken, another forty eight samples, including expiratory samples and nasal swab samples, from three animals reared in Baiji Dolphinarium were collected. Morphologic observation was implemented by Gram stain, partial 16S rDNA gene segments of bacteria were amplify with three pairs of universal primers, compared with segments reserved in Genbank, it was defined that
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