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Anthocyanins confer the wide range of colors for plants and also play beneficial health roles as potentially protective factors against heart disease and cancer. Brassica junceais cultivated as an edible oil resource and vegetable crop worldwide, thus elucidating the anthocyanin biosynthetic pathway would be helpful to improve the nutritional quality of Brassica junceathrough the breeding and cultivating of high anthocyanin content varieties. Herein, 129 genes in B. junceawere identified as orthologs of 41 anthocyanin biosynthetic genes (ABGs) in Arabidopsis thalianaby comparative genomic analyses. The B. junceaABGs have expanded by whole genome triplication and subsequent allopolyploidizatoin, but lost mainly during the whole genome triplication between B. rapa/B. nigraand A. thaliana,rather than the allopolyploidization process between B. junceaand B. rapa/B. nigra,leading to different copy numbers retention of A. thalianahomologous genes. Although the overall expansion levels ABGs were similar to the whole genome, more negative regulatory genes were retained in the anthocyanin biosynthesis regulatory system. Transcriptional analysis of B. junceawith different anthocyanin accumulation showed that BjDFR, BjTT19, BjTT8are significantly up-regulated in plants with purple leaves as compared with green leaves. The overexpression of BjTT8and these target genes which were involved in late anthocyanin biosynthesis and transport might account for increasing levels of anthocyanin accumulation in purple leaves. Our results could promote the understanding of the genetic mechanism of anthocyanin biosynthesis in B. juncea.