Six genes involved in anthocyanin biosynthesis in tartary buckwheat have been cloned, namely, FtC4H, Ft4CL, FtCHI, FtF3H, FtF3'H, and FtANS, which encode cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), chalcone isomerase (CHI), flavones 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), and anthocyanidin synthase (ANS), respectively. Then, these cDNAs were used, along with previously isolated clones for phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS), to compare gene expression in different organs, flowering stages, and maturing seeds of tartary buckwheat cultivars 'Hokkai T8' and 'Hokkai T10'. Quantitative real-time polymerase chain reaction analysis showed that these anthocyanin biosynthetic genes were most highly expressed in the stems and roots of Hokkai T10. The FtANS gene was more highly expressed than other genes during flowering and maturing seeds. In addition, the anthocyanin concentration was higher in 'Hokkai T10' than in 'Hokkai T8'; however, naringenin chalcone, a flavonoid, was absent from 'Hokkai T10' seedlings based on fluorescence microscopy.