Abstract: Pathogens are often found with Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis; YFPs) that live under captive and semi-natural conditions. To investigate the diagnosis and treatment of bacterial diseases of Yangtze finless porpoise, the pathogenic bacterium Staphylococcus aureus and Morganella morganii were isolated from naturally infected Yangtze finless porpoise that live under semi-natural conditions in Anqing Xijiang River. The drug-sensitivity tests of the pathogenic bacterium of the Yangtze finless porpoise demonstrated that pathogens are Staphylococcus aureu and Morganella morganii. The outcomes of treatments based on drug test results were effective. This study provides a good reference for the diagnosis and prevention of bacterial diseases of the Yangtze finless porpoise and dolphin.