The purpose of this study was to construct the DNA fingerprinting and query system with which to identify mung bean varieties from Northeast China. Eight primer pairs for fluorescent‐labeled simple sequence repeat markers with high polymorphism and a strong discrimination ability were used to detect 151 mung bean varieties from Northeast China. A total of 59 bands were detected, ranging from 4 to 11 with an average of 7.4. An unweighted pair group method analysis was used to cluster the mung bean varieties into five separate groups according to their genetic characteristics, which were consistent with the results of principal component analysis. Unique identification cards and barcodes with which each variety can be identified were established according to fingerprinting. A query system was also established which can provide the information and genetic relationships among some indefinite variety and mung bean varieties from Northeast China. This research will significantly assist in identification, traceability management, protection of origin, and intellectual property rights. It will also provide essential technical support for revealing the level of genetic diversity for breeding and germplasm innovation of mung bean varieties in Northeast China.