Japanese cultivated gentians (Gentiana triflora, G. scabra and their hybrids), some of the most important ornamental flowers in Japan, have vivid blue flowers that accumulate polyacylated anthocyanins such as gentiodelphin. To breed attractive flower colors in Japanese gentians, our research group has been studying the molecular mechanisms that control flower pigmentation. Flavonoids, including anthocyanins, are widely distributed in the plant kingdom and are found in almost all plant organs. Along with longstanding genetic and molecular biological analyses of flavonoid biosynthesis, recent studies have revealed that transcription activators and repressors are involved in sophisticated control of temporal and spatial flavonoid accumulation in various plant organs. In this review, we summarize recent research on the transcriptional regulation of flavonoid biosynthesis in flowers, with a special focus on our findings using Japanese gentians. We also introduce and discuss the potential application of these transcription factor genes as novel tools to engineer flower color intensity and patterns in floricultural plants.