Fagopyrum caudatum var. grandiflorum M.L.Zhou & Yu Tang is a perennial herb found in Gansu Province of China. In the present study, we combined morphological, palynological, anatomical and genetic data to clarify the taxonomic status of F. caudatum var. grandiflorum. Morphologically, in terms of flower size, achene size, leaf shape, and petiole characteristics, F. caudatum var. grandiflorum shows significant differences with F. caudatum. Its pollen grains also differ notably in size, colpi length and width, and lumina size compared to F. caudatum. Anatomically, the upper epidermis, lower epidermis, palisade tissue, spongy tissue, and leaf thickness of F. caudatum are greater than F. caudatum var. grandiflorum. Phylogenetic analysis based on ITS sequences indicates that F. caudatum var. grandiflorum has a closer genetic relationship to F. callianthum and F. lineare than to F. caudatum. Meanwhile, chloroplast regions analysis shows that F. caudatum has a closer genetic relationship with F. macrocarpum. Overall, the results from morphology, palynology, leaf anatomy, and phylogenetics support that the relationship between F. caudatum var. grandiflorum and F. caudatum should be interspecific rather than infraspecific. Considering morphological and geographic distribution, it is appropriate to recognize F. caudatum var. grandiflorum as a distinct species, renamed Fagopyrum grandiflorum (M.L.Zhou & Yu Tang) A.H.Wang & L.Tan.