The cDNA sequence of dihydroflavonol 4-reductase (DFR) gene was amplified from total RNA from the leaves of tartary buckwheat (Fagopyrum tataricum) and common buckwheat (Fagopyrum esculentum) by RT-PCR using homology-based cloning strategy. The amplified fragments were then cloned into T-vector. Sequence analysis indicated that both cDNAs had open reading frames of 1026 bp in full length, which encoded a polypeptide composed of 341 amino acids with typical structure characteristics and functional module of DFR enzyme, respectively. The nucleotide similarity of dfr gene among Fagopyrum tataricum, Fagopyrum esculentum and other plants ranged from 71% to 98%. In addition, the phylogenetic analysis based on amino acid sequence enconded by dfr gene indicated that both buckwheat varieties, Leguminosae, Moraceae and Rosaceae were classified into one class.