Objective. A multiplex polymerase chain reaction (multiplex PCR) assay was developed to detect simultaneously Salmonella sp., Shigella sp., Pseudomonas aeruginosa, Eterohaemorrhagic Escherichia (EHEC) and Vibrio prahaemolyticus in a tube. Methods. The five pairs of primers were designed and composed according to the virulence-associated, high-conservative and specific genes of these pathogens, optimized the system and condition of multiplex PCR. Results. The detection sensitivity of multiplex PCR were 10(1)cfu, 10(2)cfu, 10(2)cfu, 10(2)cfu and 10(1)cfu of one assey for EHEC, Shigella sp., Vibrio prahaemolyticus, Pseudomonas aeruginosa and Salmonella sp., respectively. The manual polluted water and 100 natural water samples were examined by multiplex PCR, and the results were clear, specific and coincident. It took six to eight hours to detect a sample. Conclusion. This multiplex PCR method would be a routine and practical protocol for detecting and identifying pathogenic microorganism from food, clinical or environmental samples. Not only was this method more sensitive, specific and efficient, but also the processing was rapid and simple. It could provide the experiment proof for the bacterial pathogens detection in water quickly and accurately. [Life Science Journal. 2008; 5(4): 47-54] (ISSN: 1097-8135).