In this study, a MYB transcription factor related to flavonoids metabolism was screened from florescence transcriptome data of Tartary buckwheat, which was named FtMYB23. Bioinformatic analysis showed that it contains a 879 bp ORF that encodes a protein of 292 amino acids. Multiple sequence analysis presented that FtMYB23 is a typical R2R3MYB transcription factor. Phylogenetic tree indicated that FtMYB23 should be gathered into the same cluster with SG5MYB subfamily members. Analysis of βgalactosidase filter paper showed transcriptional activation activity. Transgenic lines exerted increased pigmentation in seed coats, and the content of proanthocyanidins in leaves was significantly increased 4.68, 3.5 and 2.8 times of wild type, respectively (P < 0.01). Meanwhile, the expression of AtCHS, AtCHI, AtF3H, AtF3′H, AtFLS, AtDFR, AtBAN genes related to flavonoids synthesis in transgenic Arabidopsis thaliana was significantly upregulated (P < 0.05). Nevertheless, AtTT12 was dramatically down regulated (P < 0.01). Therefore, as a typical Subgroup5MYB (SG5MYB) activating transcription factor, FtMYB23 promotes the expression of key enzymes in the early stage of flavonoid biosynthesis pathway, thereby enhancing the synthesis and accumulation of proanthocyanidins.