The genus Diospyros contains more than 500 species, among them persimmon (Diospyros kaki Thunb.) is the most economically important species. However, the inter- and intra-specific genetic diversity remains unknown due to historic cultivation, domestication and introduction in different regions of China. In this study, we investigated the genetic diversity and relationship among 268 Diospyros accessions from different regions in China using start codon-targeted (SCoT) and inter-retrotransposon-amplified polymorphism (IRAP) markers. Among 268 samples, 232 accessions were D. kaki varieties and 36 were closely related species, that is, D. lotus (21), D. glaucifolia (1), D. virginiana (5), D. kaki Thunb. var. silvestris (3), D. oleifera (5) and D. deyangnsis (1). In our study, a total of 90 and 97 polymorphic alleles were obtained from nine SCoT and nine IRAP markers, respectively, and these markers displayed rich polymorphisms for evaluation of the genetic diversity among 268 samples. A study on the relationship, genetic structure and analysis of molecular variance (AMOVA) showed that inter- and intra-specific gene exchanges were frequent among/within the samples from five regions. Moreover, the genetic distance between the Southwest China (SWC) and the other regions was relatively far; the samples from North China (NC), East China (EC), South and Central China (SCC), Northwest China (NWC) regions had a relatively close relationship. The unweighted pair group method with arithmetic means (UPGMA) and population structure analysis indicated that persimmons within geographic regions were clustered together, which revealed that the samples from various regions exhibited gene exchange, and the geographical proximity of persimmons resulted in a more frequent exchange. In addition, the persimmon had a close relationship with D. kaki var. silvestris, D. deyangnsis and D. oleifera species, and exhibited a far distance with respect to D. virginiana. These SCoT and IRAP markers will be helpful for understanding of the inter- and intra-specific genetic diversity of Diospyros germplasms, which play an important role in the germplasm efficient conservation, identification and utilization for Diospyros resources.