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<i>Scutellaria baicalensis</i> Georgi is an annual herb from the <i>Scutellaria</i> genus that has been extensively used as a traditional medicine for over 2000 years in China. Baicalin and other flavonoids have been identified as the principal bioactive ingredients. The biosynthetic pathway of baicalin in <i>S. baicalensis</i> has been elucidated; however, the specific functions of R2R3-MYB TF, which regulates baicalin synthesis, has not been well characterized in <i>S. baicalensis</i> to date. Here, a S20 R2R3-MYB TF (<i>Sb</i>MYB12), which encodes 263 amino acids with a length of 792 bp, was expressed in all tested tissues (mainly in leaves) and responded to exogenous hormone methyl jasmonate (MeJA) treatment. The overexpression of <i>SbMYB12</i> significantly promoted the accumulation of flavonoids such as baicalin and wogonoside in <i>S. baicalensis</i> hairy roots. Furthermore, biochemical experiments revealed that <i>Sb</i>MYB12 is a nuclear-localized transcription activator that binds to the <i>SbCCL7-4</i>, <i>SbCHI-2</i>, and <i>SbF6H-1</i> promoters to activate their expression. These results illustrate that <i>SbMYB12</i> positively regulates the generation of baicalin and wogonoside. In summary, this work revealed a novel S20 R2R3-MYB regulator and enhances our understanding of the transcriptional and regulatory mechanisms of baicalin biosynthesis, as well as sheds new light on metabolic engineering in <i>S. baicalensis</i>.