Flavonoids are major secondary metabolites derived from the plant phenylpropanoid pathway that play important roles in plant development and human health benefits. The so-called MBW ternary complexes involved R2R3-MYB, basic helix-loop-helix (bHLH) transcription factors and WD-Repeats proteins have been reported to regulate expression of the biosynthetic genes in the flavonoids pathway. MYB4 and the closest homolog MYB7 have been suggested to function as repressors of phenylpropanoid metabolism. However, the detailed mechanism has not been fully elucidated. In this study, we revealed that in Arabidopsis MYB4 and the homologs MYB7 and MYB32 interact with the bHLH transcription factors (TT8, GL3 and EGL3) and therefore interfered the transcriptional activity of the MBW complexes. In addition, MYB4 can also inhibit flavonoids accumulation by repressing expression of the gene encoding Arogenate Dehydratase 6 (ADT6), which catalyzes the final step of the biosynthesis of phenylalanine, the precursor of flavonoid biosynthesis. Interestingly, our data showed that MYB4 potentially repressed not only the conventional ADT6 encoding the plastidial enzyme but also the alternative isoform encoding the cytosolic enzyme. We suggest that MYB4 plays dual roles in controlling flavonoid biosynthesis in Arabidopsis.