The potential risk of foodborne pathogens in the ballast water to act as a major vector for public health and port ecological environment has long been recognised. At present, the foodborne pathogens is detected by culture and biochemical identification, Real-time PCR and other methods, which can not detect multiple pathogenic bacteria. This study focused on the application of a high-throughput DNA microarray chip p that can detect 12 kinds of foodborne pathogens. By the chip,every control strain of pathogen can be specifically detected without inferring with other organism. In the level of DNA molecule, the chip can detect the minimal 110 copies for the most sensitive Shigella, and the maximal 7000 copies for Staphylococcus aureus. Pathogens with copies of 10⁴-10⁵, can be detected directly by the thermal lysis bacteria. ballast water supplied with five kinds of pathogens of 1cfu/ml can be detected in 2 hours followed with several hours of culture. the method for the simultaneous foodborne pathogens besides Staphylococcus aureus,Salmonella spp,and Shigella spp, Listeria monocytogenes, Escherichia coli O157:H7, Vibrio parahaemolyticus,Vibrio cholera, Bacillus cereus Clostridium perfringens, Campylobacter, Cronobacter sakazakii, Shigella Castellani could be detected. The minimum limit of the chip is higher than the PCR methods, while the chip of this study was high-throughput, rapid and efficient in the detection,which could be a useful method for the simultaneous detection of foodborne pathogens in the ballast water