Background <p>Seed shattering is a crucial adaptive trait in wild plant species but is undesirable in domesticated crops. In this study, we investigated the anatomical and molecular mechanisms underlying seed shattering in common buckwheat (Fagopyrum esculentum) and explored its genetic control. Previous research has shown that seed shattering in <i>F. esculentum</i> follows a monogenic inheritance pattern. To pinpoint the genomic region associated with this trait, we analyzed an F₂ progeny derived from a cross between wild ancestor of common buckwheat - <i>Fagopyrum esculentum</i> ssp. <i>ancestrale</i> and the cultivated variety - <i>Fagopyrum esculentum</i> cv. Dasha.</p> Results <p>Anatomical analysis revealed that both shattering and non-shattering phenotypes possess an abscission zone (AZ); however, in non-shattering plants, the AZ remains underdeveloped and inactive. Histological observations indicated that AZ formation begins during early bud development. Transcriptomic analysis across four developmental stages (early bud, late bud, flower, and fruit) identified abscisic acid regulation, ethylene signaling, and cell wall modification as key factors in AZ differentiation. Unexpectedly, many genes typically associated with abscission layer activation showed increased expression at the flower stage rather than the fruit stage, suggesting that AZ activation occurs earlier than anticipated. We also provided preliminary data on the localization of the gene responsible for shattering in wild buckwheat and reviewed candidate genes.</p> Conclusion <p>Our results provide new insights into the structure of abscission zone in buckwheat and into molecular mechanisms underlying seed shattering in buckwheat. We identified key pathways involved in abscission zone differentiation and performed the initial localization of the causative gene.</p>