Buckwheat sprouts are considered an excellent dietary source of phenolic compounds. The time duration and amount of light for sprouting strongly affect the nutritional quality of sprouts. In this study, these two factors were investigated in two cultivars of tartary buckwheat sprouts: Hokkai T8 and T10. The transcriptional levels of flavonoid biosynthetic genes were investigated in light/dark- and dark-treated sprouts. Among the main flavonoid biosynthesis structural genes, FtPAL, Ft4CL, FtF3H, FtDFR, and FtANS exhibited higher transcriptional levels than others as compared to that of a housekeeping gene (histone H3) during sprouting; FtF3'H1, FtF3'H2, FtFLS2, and FtANS were substantially upregulated at 2, 4, and 6 days in light/dark-treated T10 sprouts than in dark-treated ones. However, FtDFR was downregulated in 8 and 10 day old light/dark-treated sprouts of both cultivars. High-performance liquid chromatography (HPLC) analysis revealed that increasing the culture time did not affect the accumulation of flavonoids or anthocyanins. However, light contributed the production of anthocyanins in Hokkai T10 sprouts. The anthocyanins included cyanidin 3-O-glucoside, cyanidin 3-O-rutinoside, and delphinidin-3-O-coumarylglucoside, which were identified by HPLC and electrospray ionization-tandem mass spectrometry. Instead of anthocyanins, Hokkai T8 sprouts produced large amounts of 4 flavonoid C-glycosylflavone compounds in both light/dark and dark conditions: orientin, isoorientin, vitexin, and isovitexin. These results indicate that these two types of tartary buckwheat sprouts have different mechanisms for flavonoid and anthocyanin biosynthesis that also vary in light/dark and dark conditions.