Common buckwheat is a nutritionally dense minor grain crop. However, the self-incompatible (SI), shattering, and low yield limits its wide cultivation. In this study, the hybrid experiments were performed to a) identify self-compatible parental material with non-shattering hybrid offspring, b) investigate the heterosis, and c) evaluate the relationship between heterosis and parental genetic distances (GD) in common buckwheat. As a result, nineteen self-compatible wild common buckwheat pure lines were identified with non-shattering hybrid offspring, and 58 hybrids were produced by single crossing between these 19 pure lines and four common buckwheat cultivars. For five agronomic and one quality trait, the 58 hybrids showed significant mid- and high-parent heterosis in common buckwheat. Furthermore, the GD values among parental lines were successfully calculated based on the random-amplified polymorphic DNA (RAPD) and sequence tagged site (STS) molecular markers. Non-significant relationship was observed between heterosis and parental GDs for any trait under this study, suggesting that the parental GDs could not be reliable to predict the heterosis in common buckwheat. However, present results are still valuable for further research in heterosis and parents-pair selection for improvement in common buckwheat through cross-breeding program.