Effective conservation strategies aimed to protect crop genetic resources require multiple sources of information. We used a combination of AFLP genotyping and farmer surveys to understand the extent, distribution and management of tartary buckwheat (Fagopyrum tataricum Gaertn.) diversity in its center of origin in Yunnan Province, China. We found genetic evidence of gene flow in tartary buckwheat throughout the study area, with small but statistically significant regional and village-level components. We also found genetic differentiation by seed color. Although most farmers reported exchanging seed in localized kinship networks, our results imply homogenizing gene flow is occurring. Yi ethnic farmers tend to plant more buckwheat than non-Yi farmers, and we found that in some communities, Yi farmers serve as seed sources for farmers of other ethnicities. Different tartary buckwheat varieties did not have different end uses; rather farmers maintained varietal diversity in order to protect crop yield and quality. Individual farmers’ seed exchange practices reflect their ideas about components of seed quality, as well as priorities in protecting buckwheat yield. From the standpoint of genetic resources conservation, the presence of a culturally rich farmer exchange network and hierarchical structuring of tartary buckwheat genetic diversity demonstrates the importance of maintaining an interlinked community of tartary buckwheat farmers in Yunnan.