Tartary buckwheat seeds are highly nutritious and excellent dietary sources of phenolic compounds. Rice-tartary buckwheat is a special type of tartary buckwheat with a non-adhering hull trait. Here, we investigated the levels of expression of genes involved in the flavonoid biosynthetic pathway in common tartary and rice-tartary buckwheat. The flavonoid biosynthetic genes, from FtPAL to FtANS, showed different expression levels, especially in the reproductive organs of the 2 cultivars. The transcription levels of these genes, except FtC4H and FtANS, were higher in the mature seeds of rice-tartary buckwheat than in those of common buckwheat. We also analyzed the flavonoid compounds found in the different organs of common tartary buckwheat and rice-tartary buckwheat. Even though the content of rutin was similar in both the cultivars, the distribution of the 3 main flavonoids-rutin, quercetin, and kaempferol-was different in the 2 cultivars, both across organs and within the seed. These results indicate that in the 2 tartary buckwheat cultivars, flayonoid biosynthesis is carried out by different mechanisms. (C) 2012 Elsevier Ltd. All rights reserved.