Abstract: Eestablishment of molecular identity is beneficial to effectively serve the preservation and utilization of the germplasm in flowering Chinese cabbage. In this study, the fluorescent microsatellite -anchored fragment length polymorphism (MFLP) technique was utilized to genotype 36 accessions of the flowering Chinese cabbage germplasm collected from different parts of China, and 18 appropriate primer pairs amplified stably and unambiguously polymorphic bands were chosen from 200 selective amplification primer combinations to detect the polymorphic alleles among the accessions. The results showed that the polymorphic alleles for 18 primer pairs ranged from 3 to 31 with the average of 12.5 per primer combination. Polymorphism information content (PIC) and marker index (MI) ranged in 0.26-0.98 and 0.8- 30.4, respectively. The principal coordinate analysis (PCA) showed that 36 accessions could be clearly distinguished by 18 primer combinations, which divided into 3 groups based on genetic similarity. According to the principal of distinguishing accessions with the less primer pairs, three primer pairs including tfCCTA(CA)7/mAAG, tfGGTC(ATT)5/mCAA and tfCCTA (CA)7/mCTC with the highest values of PIC and MI were selected as the core primer combinations. Based on the binary data of the allele variants (allele present is 1, absent is 0) of the accessions, the molecular identity for each accession of flowering Chinese cabbage was established by converting the corresponding binary data into the simple and intuitive hexadecimal data.