The invention provides a gene chip for detecting various seawater cultured animal pathogenic bacteria and its application. The pathogenic bacteria include: Vibrio anguillarum, Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, Vibrio fischeri, Vibrio splendidus, Vibrio riverina, Vibrio vulnificus, Vibrio cholerae non-O1, Vibrio mimicus, Vibrio salmonicida, Aeromonas hydrophila, Aeromonas sobria, Aeromonas salmonicida, Edward tarda Bacillus, Edwardsiella catfish, Renalobacter salmonidum, Mycobacterium marinum, Pseudomonas, Streptococcus.