Abstract:The current study was to develop a PCR-based method to detect Enterobacter cloacae and Enterobacter aerogenes in Macrobrachium rosenbergii. Two pairs of primers targeted sequences located within the omp A gene of E. cloacae and gyr B gene of E. aerogenes were used to detect E. cloacae and E. aerogenes. Samples collected from infected larvae were detected with the developed PCR method. The expected DNA fragments of 385 bp and 201 bp were from E. cloacae and E. aerogenes, respectively, and no PCR products were amplified from other bacterium. The sensitivity test showed that the detection limits of PCR were 103 CFU/ml for E. cloacae and 102 CFU/ml for E. aerogenes. In addition, the detection results of larval samples were consistent with the actual case of the infectious disease. In summary, the PCR diagnostic method was specific and sensitive and is a reliable tool for identification of E. cloacae and E. aerogenes in infected samples with a little time and cost, which would play an important role in quick diagnose, epidemiology investigation and SPF populations construction of the giant freshwater prawn.