Mung bean is an important grain-legume crop and its sprout is an economical and nutrient vegetable for public, but the genetic regulation for anthocyanin which is an antioxidant in mung bean remains elusive. In our study, we characterized a subgroup 6 R2R3-MYB anthocyanin activator VrMYB90 and a subgroup 4 R2R3-MYB anthocyanin repressor VrMYB3 which synergistically function in regulating anthocyanin synthesis with VrbHLHA transcription factor. Over-expressed VrMYB90 protein activates expression of VrMYB3 and VrbHLHA in mung bean hair roots, as well as promotes VrDFR and VrANS transcript level by directly binding to the corresponding promoters by specific motifs (CAACTG and CCGTTG). VrMYB90 interacts with VrbHLHA to enhance its regulatory activities on VrDFR and VrANS. Furthermore, the interaction between VrMYB3 with VrMYB90 and VrbHLHA could result in the restriction of anthocyanin synthesis to prevent excessive anthocyanin accumulation. Our results demonstrate that the VrMYB90 protein, in conjunction with VrMYB3 and VrbHLHA, forms a key regulatory module to fine-tune anthocyanin synthesis in mung bean.