Abstract: Specific primers and probes based on the 5' flanking sequence of exogenous fragments of genetically modified( GM)soybean DAS44406-6 and endogenous Lectin gene of soybean were designed. A multiplex real- time PCR for the detection of GM soybean DAS44406- 6 and endogenous Lectin gene of soybean simultaneously had been developed. The specificity,sensitivity and stability of this method had been tested by 15 GM soybean,3 GM maize,1 GM rape,1 GM rice and 1 non- GM soybean.Results indicated that this multiplex real- time PCR method could accurately detect target from 20 GM samples and 1non- GM sample,which was in accordance to the predicted results..The sensitivity of this method was 0.01%.The repeatability test showed that the standard deviation( SD) of the Ct value ranged from 0.050 to 0.222 and the relative standard deviation( RSD) ranged from 0.169% to 0.677% of the 9 replicates about 4 concentration DNA templates,which were all in acceptable range.In conclusion,this multiplex real- time PCR method was high specific,sensitive and reliable,and would be an effective tool for the detection of GM DAS44406-6 in the laboratory of CIQ( China entry- exit inspection and quarantine bureau,CIQ).