This study attempted to identify SSR markers that can be used to validate the authenticity of F1 hybrids between buckwheat species and for the future research on hybrid breeding of buckwheat. By employment of 235 pairs of SSR primers, we performed PCR amplification using five parental lines of buckwheat to identify these polymorphic markers. We applied these polymorphic markers and morphological analysis to validate if the interspecific plants were hybrids. As a result, 2 pairs of polymorphic primers (SSR2159/58 and SSR6790/89) were identified, and three true hybrids were identified, including F.tataricum var. Daku No.1 × F. cymosum, F. tataricum × F. cymosum, F. giganteum × F. cymosum. Thus, SSR markers can be used for identifying interspecific hybrids of buckwheat.