Abstract: In order to reveal antibacterial effects of Berberine on three aquatic pathogens and its mechanisms, we determined the minimal inhibitory concentration/the minimal bactericidal concentration(MIC/MBC) of Berberine on Vibrio parahaemolyticus, V.alginolyticus and Aeromonas hydrophila, as well as the effects of Berberine on the cell morphology and the cell growth curve of three bacteria. The results show that the MIC and MBC of Berberine on V.parahaemolyticus, V.alginolyticus and A.hydrophila are 0.391 mg · mL^-1 and 0.391 mg · mL^-1, 0.391 mg · mL^-1 and 0.781 mg · mL^-1, 0.781 mg · mL^-1 and 1.563 mg · mL^-1, respectively. These results indicate that Berberine has significant antibacterial effects on tested bacteria, especially its inhibitory effect on V.parahaemolyticus . Besides, 1.00 mg · mL^-1 of Berberine can seriously destroy the cell morphology of pathogens, and extend the lag phase of pathogens to 2~7 h, which suggests that the antibacterial effects of Berberine might be achieved through affecting the cell structure and growth of pathogens. In conclusion, Berberine is a potential drug against aquatic bacterial diseases.