The invention discloses a method for establishing DNA molecular tags of Yunjing series rice varieties. According to the method, 6 pairs of specific primers for identifying the Yunjing series rice varieties are provided, the Yunjing series rice varieties are identified with fewest primers at the wide genome coverage degree, DNA molecular tags of all the Yunjing series rice varieties can be constructed with fewest primers, the heavy workload and the high detection cost are reduced, the Yunjing series rice varieties can be distinguished from other Yunnan plateau japonica rice varieties, and meanwhile, the Yunjing series rice varieties can be distinguished one by one. According to the method, DNA fingerprint data, obtained through amplification, of the Yunjing series rice varieties and acquired basic commodity information are subjected to digital coding assignment to form 2-dimensional code expression, the DNA molecular tags of Yunjing series rice varieties can be obtained, uniqueness, identifiability and traceability of variety identification and scientific seed management can be realized, and the DNA molecular tags are marked on commercial seed packaging and used for faking prevention and tracing of good rice variety seeds.