Fagopyrum cymosum is a perennial herb of the family Polygonaceae, which has a very high medicinal value because its swollen stems are rich in flavonoids. Wild Fagopyrum cymosum is widely distributed in China, especially in southwestern areas such as Yunnan, Guizhou, Sichuan. Our research group conducted a 20-day study in Yunnan and collected wild Fagopyrum cymosum resources from 14 different regions in Lijiang, Dali and Kunming. There were some differences in the plant or fruit morphology of wild golden buckwheat in different regions, which may be related to the geographical environment and climatic conditions. The contents of total flavonoids, rutin and quercetin in the swollen stems of wild golden buckwheat were measured by spectrophotometry and high performance liquid chromatography (HPLC). Results showed that the flavonoid contents of the swollen stems from different regions were remarkably different. Using ITS and matK molecular markers, genetic diversity and genetic relationship analysis were carried out, and it was found that the classification had a significant relationship with regional altitude.