Chestnuts are important economic forest tree species with enormous application value in the wood, medicine, and chemical industries. Currently, the limited genome-wide SSR molecular marker information on chestnut resources significantly limits research on genetic diversity and identification of chestnut resources. To address this issue, we used GMATA to screen simple sequence repeat (SSR) markers throughout the Chinese chestnut genome. A total of 312,302 molecular markers were obtained with a density of 434.38/Mb. Subsequently, all SSR markers were examined for polymorphism using the HipSTR program and 138,208 polymorphic loci were finally obtained. To verify the identification ability of the developed SSR, we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient chestnut resources from the Yanshan Mountains. The results showed that only 6 pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees, showing that the developed markers have high identification potential. We then evaluated the inter-specific universality and polymorphism of these markers using three species, including 91 chestnut plants. The molecular markers amplified 94% of the interspecies with a PIC value of 0.859. Cluster analysis revealed that testing resources using these developed markers can be well differentiated and these markers have been widely used to identify interspecific boundaries. These results proved that the developed molecular markers have the potential for genotypic diversity, which can provide references for genetic diversity research, variety identification, kinship analysis, selection of good products, and construction of core germplasm resources of chestnut and even chestnut plants. They lay a solid foundation for the molecular design of hybrids to improve breeding and develop germplasm resources.