Abstract:o investigate the prevalence of pathogenic Vibrio. and Aeromonas hydrophila in aquaculture animals in flowing through systems in Nanchang, animals were sampled over an 18-month period between March 2009 and September 2010. Seven pairs of primers were designed for toxin sub-unit A (ctxA) gene, O139 special gene, O1 special gene, tcpA gene, toxR gene, haemolytic gene, vvhA gene and aerolysin(aerA) gene. Specific PCR was established to simultaneously detect these 7 genes. Strains of Vibrio cholerae, V. parahaemolyticus, V. vulnificus and Aeromonas hydrophila can be detected and differentiated by the size and numbers of specific PCR products through electrophoresis bands examination. In 1 440 tested samples, 17 samples were Vibrio parahaemolyticus positive (1.74%), 25 samples were Vibrio cholerae positive (1.18%), and no Aeromonas hydrophila and Vibrio vulnificus were found in the samples. The results of PCR detection were consistent with those of the traditional culture methods. The results indicated that the levels of pathogenic Vibrio in Nanchang area were very low, while the levels of pathogenic Vibrio in Amyda Sincnsis and Rana catesbeiana were relatively high.