To fully understand the distribution and variation patterns of wild Fagopyrum dibotrys (D. Don) Hara resources, this study conducted field investigations on seven wild populations collected from central and northeastern Yunnan, and performed a systematic diversity analysis based on phenotypic characteristics, secondary metabolites (flavonoids), and SSR molecular markers. The results showed that the distribution density and population size of Fagopyrum dibotrys were relatively high in northeastern Yunnan, while those in central Yunnan were low and scattered, which may be related to the high degree of industrialization in central Yunnan. Wild Fagopyrum dibotrys in this region exhibited abundant population variation and high plasticity in both phenotypic traits and secondary metabolite profiles. Genetic diversity analysis revealed that different populations possessed varied levels of genetic diversity. The expected heterozygosity (He) of these populations ranged from 0.1435 to 0.2735, and the Shannon"s information index (I) varied from 0.2060 to 0.3985. The Ludian population showed the highest genetic diversity, suggesting that it may represent a genetic diversity center of Fagopyrum dibotrys in central and northeastern Yunnan. The genetic differentiation coefficient (Fst) among populations ranged from 0.0203 to 0.2006. The Zhaoyang population exhibited relatively strong genetic differentiation from other populations, which may be associated with the unique climate and geographical location of its distribution area.This study clarified the background diversity and population differentiation characteristics of wild Fagopyrum dibotrys in central and northeastern Yunnan, providing a scientific basis for the precise conservation and innovative utilization of this species.