We isolated an ortholog (LjMYB12) of the Arabidopsis R2R3-MYB transcription factor (TF) gene from Lotus japonicus to investigate the regulation of flavonoid biosynthesis, which is driven by many paralogous genes in L. japonicus. We characterized the spatial and temporal expression of LjMYB12 in leaves, stems, roots, flowers, immature seeds, seedling leaves, and seedling roots. Expression was much higher in flowers than in other tissues. To verify the relationship between the expression of LjMYB12 and that of flavonoid biosynthesis genes, we generated transgenic L. japonicus plants overexpressing LjMYB12. Overexpression of LjMYB12 resulted in the upregulation of genes for a chalcone synthase paralog (CHS1), flavanone 3-hydroxylase, and flavonol synthase. Interestingly, LjMYB12 strongly activated CHS1 but did not activate other CHS paralogs. This result suggests differences in the spatial or temporal activation of CHS paralogs by R2R3-MYB TFs. Molecular characterization of R2R3-MYB TFs in L. japonicus will reveal the effects of gene duplication on the regulation of diverse flavonoid biosynthesis.