Based on TPM13SSR fluorescent capillary detection technology, we analyzed the genetic diversity of 99 registered sweetpotato varieties. The “01” database of the registered varieties was established by SSR markers. The Nei genetic distance among different varieties was calculated using the DPS software. The NeighborJoining method in MEGA was used for cluster analysis, and the genetic structure of the accessions was analyzed by the admixture ancestry model in Structure software. The genetic composition of the varieties and the genetic relationship among the varieties were discussed, which revealed the similarity of the sweetpotato varieties at the DNA level and provided references for variety evaluation, excellent parent selection and variety improvement. The results showed that： (1) a total of 162 reproducible bands were amplified from 28 primer pairs with an average of 5.57 bands and polymorphic rate was 96.30%. (2) The dendrogram of 99 registered varieties was constructed. And the genetic distance of 99 varieties ranged from 0 to 0.464 6 with an average of 0.307 7. Cluster analysis at 0.267 0 genetic distance can divide 99 varieties into three groups. Sweetpotato varieties from the same agroecological zones or close relationship were clustered in the same groups. The varieties from different agroecological zones were relatively scattered in different groups. (3) The genetic background among accessions is relatively narrow. And similarity of some varieties is higher in some certain of the ecological zones. By population structure analysis, the 99 varieties were divided into three subgroups. Clustering results were in coincident with the results of population structure. The 31 accessions have a high degree of mixed ancestry and complex genetic background.