Abstract: To explore the role of glutathione S-transferase gene(GST)in the accumulation of anthocyanin in Brassica juncea, one GST gene related to the anthocyanidin accumulation was cloned from near-isogenic lines of B. juncea with purple stalk and green stalk, and named as BjGSTF12. In this study, the bioinformatics characteristics of BjGSTF12 encoding protein and promoter were analyzed, the expression level of BjGSTF12 and the relationship with total anthocyanidin content were analyzed in B. juncea lines with purple stalk and green stalk. The results were as follow:(1)BjGSTF12 genes from B. juncea were successfully cloned, whose the full length of BjGSTF12 in genome and cDNA was 808 bp and 651 bp, encoding a protein of 216 amino acids. The BjGSTF12 contained the typical domains of GST proteins, namely GST_N and GST_C. However, their sequences of BjGSTF12 did not exhibit any differences between the two lines of B. juncea.(2)BjGSTF12 was closely related to AtGSTF12 in Arabidopsis, and both belonged to the φ subfamily of GST family.(3)The BjGSTF12 promoter sequences were cloned from two Brassica juncea strains of green stalk and purple stalk, and they exhibited four base mutations/insertions. However, the types and numbers of cis-acting elements did not show obvious differences between the two strains, including nine MYB transcription factor binding sites, one hormone response element, and three abiotic corresponding elements.(4)The total anthocyanidin content in B. juncea of purple stalk was significantly higher than that in green stalk ones, and the expression levels of BjGSTF12 in two lines were found to be similar to the total anthocyanidin content in both lines.(5)Protein interaction network analysis revealed that BjGSTF12 may interact with the key enzymes of anthocyanidin biosynthesis, glycosylation modification, and transporter proteins. In summary, BjGSTF12 is likely to play a key role in the accumulation of anthocyanidin in B. juncea by regulating its biosynthesis, modification, and transportation through interactions with other proteins. This study provides a theoretical reference for further study on the function of GST and the mechanism of anthocyanidin accumulation in B. juncea.