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<i>Salvia miltiorrhiza</i> Bunge is one of the most famous traditional Chinese medicinal plants. The two most important classes of pharmaceutically relevant compounds in <i>S. miltiorrhiza</i> are phenolic acids and tanshinones. The MYB family of transcription factors may efficiently regulate the secondary metabolism in plants. In this study, a subgroup 4 R2R3MYB transcription factor gene, <i>SmMYB4</i>, was isolated from <i>S. miltiorrhiza</i> and functionally characterized using overexpression and a RNAi-mediated silencing. We achieved a total of six overexpressions and eight RNAi transgenic lines from the <i>Agrobacterium</i> leaf disc method. The content of the total phenolics, rosmarinic acid, and salvianolic acid B markedly decreased in the <i>SmMYB4</i>-overexpressing lines but increased in the <i>SmMYB4</i>-RNAi lines. The content of the total tanshinones, cryptotanshinone, and tanshinone IIA decreased in the <i>SmMYB4</i>-overexpressing transgenic lines but increased in the <i>SmMYB4</i>-RNAi lines. A gene expression analysis demonstrated that SmMYB4 negatively regulated the transcription of the critical enzyme genes involved in the phenolic acid and tanshinone biosynthesis. The genetic control of this transcriptional repressor may be used to improve the content of these bioactive compounds in the cultivated <i>S. miltiorrhiza</i>.