Abstract: Buckwheat was originated in southwest of China, where exists a large number of buckwheat landraces and wild relatives. This study analyzed the genetic diversity of 81 samples of buckwheat and its wild species with SSR molecule makers. The results indicated that 84 alleles were detected among 81 samples of 11 species by 19 pairs of SSR primers, averaged 4.421 alleles by each pair of SSR primers. The average Shannon's information index of 19 pairs of SSR primers was 0.985, while the average PIC was 0.478. The similarity coefficient range of 81 buckwheat samples were 0.500 to 1.000. The analysis found that the large-seed group grain(F.esculentum, F.esculentum ssp.ancestralis, F.tataricum, F.kashmirianum, F.cymosum) were more closely related to F.urophyllum. At the position 0.732 of the similarity coefficient, all samples can be divided into four categories by the clustering analysis. The first category is composed of F.gracilipes, F.gracilipes var. odontopterum, F.leptopodum, F.leptopodum var.grossii and F.urophyllum; the second category is made up of F.esculentum, and F.esculentum ssp. ancestralis, the third category is composed of F.cymosum only, and the fourth category includes F.tataricum and F. kashmirianum. However, the pellets can be obviously distinguished into buckwheat F.leptopodum var.grossii, F.urophyllum, F.gracilipes and F.gracilipes var.odontopterum. At the position 0.920 of genetic coefficient, F.leptopodum var.grossii, F.urophyllum, F.gracilipes var. odontopterum and F.gracilipes were clearly distinguished in the small-seed group. This research shows that SSR primers have high level of polymorphism and is able to detect the genetic diversity of buckwheat and its wild species. The results provided a scientific basis for analyzing the genetic relationships and studying the origin and evolution of buckwheat.