【Objective】Cinnamomum japonicum is a kind of protected tree species with important economic value, wild C. japonicum is a valuable genetic resource for breeding and improvement, and also is an important plant genetic resource in China. This study explored the genetic diversity and population spatial distribution pattern of C. japonicum resources in China, and laid a theoretical foundation for the protection and utilization of the resources.【Method】Specific focus amplified fragment sequencing (SLAF-seq) was performed on 30 individuals from seven populations of five provinces or municipality including Zhejiang, Anhui, Henan, Chongqing and Yunnan to develop SLAF and SNP(single nucleotide polymorphism) markers. 【Result】A total of 100.78 Mb reads data were obtained from 30 samples. After clustering the reads of different samples, a total of 1 296 000 SLAF tags were obtained. The average sequencing depth of each sample was 15.11. 377 250 SLAFs were polymorphic among different samples, and 3 409 402 SNPs were obtained from the polymorphic SLAF tags. After filtering, 268 821 population SNPs with high consistency were finally obtained. Phylogenetic analysis of these SNPs showed that C. japonicum was evolved from eastern to western China. Phylogenetic, principal component and population structure analysis all showed that the intra-population variation of the seven natural populations was smaller than the inter-population variation. The 30 individuals can be divided into two large groups, among which, the first group contained the resources collected from the second ladder of China, and the second contained resources from the third ladder of China. The two groups were separated by the Great Khingan-Taihang Mountains-Wushan Mountains-Xuefeng Mountain range. The second group can be further divided into three small subgroups, among which, those from Anhui Taoling and Zhejiang Province were included in the first subgroup, those from Anhui Huoshan were included in the second subgroup, and those from Henan Province were included in the third subgroup. The first and the second subgroup were separated by the Yangtze River. 【Conclusion】The barriers caused by mountains and lakes are important factors of the genetic differentiation of C. japonicum resources. This study reveals for the first time the genetic structure and geographical variation of C. japonicum, providing a theoretical basis for the effective utilization and scientific protection of the resources of C. japonicum.