Applied with the SRAP molecular labeling method and 15 selected primer combinations, this paper analyzes 23 cultivars of Castanea henryi and 17 populations resources of wild Castanea henryi in 5 provinces (Hunan, Zhejiang, Sichuan, Guizhou and Fujian), aming to provide a basis for genetic background analysis and germplasm innovation of Castanea henryi. A total of 221 sites were amplified in 17 wild Castanea henryi populations, with the average number and ratio of polymorphic loci being 155.06 and 70.16%. The number of total genetic diversity index (Ht), intra-population genetic diversity index (Hs), Nei’s genetic diversity index and Shannon’s information index are respectively 0.3636, 0.2466, 0.2460 and 0.3677, indicating relatively high genetic diversity and variability of wild Castanea henryi populations. Among them, the polymorphic rate of Hengshan (HS) population is the highest, which accounts for 85.07%; the polymorphic rate of population in Jishou Brook Village counts secondarily 83.26%. This evidence suggests that populations in Hengshan and Jishou (JS) have the richest genetic diversity in Hunan province. UPGMA cluster analysis shows that Xijiang population in Liuyang and Hengshan(HS) population bear the closest genetic similarity and relationship, while the contrary is the case of Liping population in Guizhou (GZ) and Yuetianzhen population in Yueyang. The polymorphic rate of 23 varieties of Castanea henryi is 89.14% and the genetic similarity coefficient is between 0.66 and 0.85. At coefficient 0.66, Dajianzui alone are clustered into one category, which reflects there is a big difference in genetic basis between Dajianzui and others; at coefficient 0.85, Huali2 and Tiezhui are clustered into one category, implying they share the closest relationship with minimum genetic diversity. In addition, during the research, we have built a SRAP digital fingerprint for the 23 varieties of Castanea henryi by using 4 primer combinations, namely Em1-Me2, Em2-Me1, Em2-Me2 and Em2-Me3. Thus providing references for rapid identification of Castanea henryi varieties.