Common buckwheat (Fagopyrum esculentum) is an annual self-incompatible plant that is widely grown. The genusFagopyrumcomprises more than 20 species, includingF. cymosum, a perennial that, unlike common buckwheat, is highly resistant to excess water. In this study, we developed interspecific hybrids betweenF. esculentumandF. cymosumvia embryo rescue, to improve undesirable traits of common buckwheat, such as low tolerance to excess water. The interspecific hybrids were confirmed by genomicin situhybridization (GISH). We also developed DNA markers to confirm the identity of the hybrids and if genes derived from each genome were inherited by the next generation. Observations of pollen indicated that the interspecific hybrids were essentially sterile. Unpaired chromosomes and abnormal segregation during meiosis were likely responsible for the pollen sterility of the hybrids. These findings could facilitate buckwheat breeding to produce lines that can withstand harsh environments with wild or related species in the genusFagopyrum.