Hairy roots were obtained after inoculating sterile young stems of Fagopyrum tataricum with Agrobacterium rhizogenes R1000. The established roots displayed two morphological phenotypes when cultured on hormone-free medium containing Murashige-Skoog salts and vitamins. The thin phenotype had a higher growth rate than the thick phenotype. Further, the phenolic compound content of the thin phenotype was higher than that of the thick phenotype. In terms of their total dry weight, the thin phenotype produced an almost double amount of (-)-epigallocatechin as well as more than 51.5% caffeic acid, 65% chlorogenic acid, and 40% rutin compared to the thick phenotype after 21 days of culture. Therefore, selection of the optimal morphological phenotype of hairy roots of tartary buckwheat is an important factor for improved phenolic compound production