In order to decipher the genetic diversiy of persimmon germplasms, a total of 112 persimmon cultivars (Diospyros kaki) collected from Shaanxi province, 16 date plums (D. lotus) from Shaanxi and 11 persimmon cultivars from Henan province were investigated by using ten SCoT markers with high polymorphism and qualified reproducibility. The statistical assessments including polymorphisms, cluster analysis, principal coordinate analysis, population structure analysis and genetic diversity analysis was analyzed according to the geographic regions of genotypes. A total of 99 polymorphic marker loci were obtained from 10 pair SCoT primers. By cluster analysis, 16 date plums were assigned to an independent cluster, differing with the persimmon cultivars. Persimmon cultivars from Henan province and Shaanxi province are clustered together and have a close genetic distance. Although the genetic structure analysis implied an exchange on genetic components among 112 persimmon cultivars in various regions of Shaanxi Province, the genetic diversity remained limited. The cultivars from both Baoji and Xi'an cities represented the highest genetic diversity, while the lowest diversity was observed in these of Southern Shaanxi. Thus, the results could facilitate better understanding of genetic contributions in varieties, and provide a scientific theoretical basis for further investigating the persimmon resources in Shaanxi Province.