Abstract: Objective To establish a duplex MGB real-time quantitative PCR (qPCR) assay for detection of ISCR1 related complex class 1 integron in bacteria. Methods The qPCR primers and probe designing was according to int1 and ISCR1 sequences in ISCR1 related complex class 1 integron. The specificity and the sensitivity of this qPCR assay were evaluated by using common pathogens and target genes containing recombinant plasmids, respectively. Results The established duplex MGB real-time qPCR assay showed good specificity. The detection limit of this qPCR assay for int1 and ISCR1 were determined to be 5.89101 copies/l and 4.13101 copies/l, respectively. Conclusion The new duplex MGB qPCR assay established in this study could be used in ISCR1 related complex class 1 integron detection and as a simple and convenient method for multi-drug resistance detection in both laboratory and large-scale surveillance.