Abstract: 【Objective】To clarify the genetic relationship of local Sect. Thea(L.) Dyer resources in Guizhou, and to provide scientific basis for their protection and utilization.【Method】A total of 41 Sect. Thea(L.) Dyer resources collected from different regions of Guizhou and 18 tea plant varieties bred from Guizhou and other provinces that kept by Institute of Tea, Guizhou Academy of Agricultural Sciences were used as materials. The genotyping-by-sequencing(GBS) was used to detect the single nucleotide polymorphism(SNP) sites in their genomes, and the genetic characteristics of the 59 Sect. Thea(L.) Dyer resources were analyzed based on the obtained high-quality genomic SNP sites.【Result】A total of 45.84 Gb clean reads were obtained from the 59 Sect. Thea(L.) Dyer resources, with an average of 795.6 Mb per material, accounting for 26.5% of the improved version of tea reference genome(2.93 Gb), and the average alignment rate was 72.62%. A total of 248772 high-quality genomic SNPs were obtained, of which 83.98% and 16.02% were distributed in intergenic region and genic region, respectively. There were 22614 SNP sites distributed in introns, 15038 SNP sites distributed in exon regions, and 2203 SNP sites distributed in untranslated regions(UTR). The results showed that the observed heterozygosity(Ho) of them ranged from 0.016 to 0.081, the expected heterozygosity(He) was 0.006 to 0.064, and F value was-0.331 to 0.737. The 59 samples were divided into three groups based on principal component analysis(PCA), phylogenetic tree construction and genetic structure analysis. Among them, all of the Camellia sinensis were in one group, C. remoterrata and C. tachangensis were in one group, and the nine C. costata were in one group. However, C. remoterrata and C. tachangensis and the C. tachangensis from two different regions could be further divided into different independent subgroups, and the C. sinensis var. assamica(CSA) and C. sinensis var. sinensis(CSS) were also in the different branches of evolutionary tree. Additionally, based on the phylogenetic tree, the genetic relationships between C. costata and C. remoterrata or C. tachangensis were more closer to that between C. costata and C. sinensis. The gene structure analysis showed that there was a fusion genetic background among the four classifications of Sect. Thea(L.) Dyer resources(C. sinensis, C. remoterrata, C. tachangensis and C. costata) used in this study. According to geographical origin and germplasm type, the 59 Sect. Thea(L.) Dyer resources were divided into 11 groups, and the gene flow analysis showed that there was a low level of gene flow among different groups and a high level of gene flow within the group.【Conclusion】There are obvious differences among different Sect. Thea(L.) Dyer groups at the genomic level. Based on the gene-tic structure, C. tachangensis and C. remoterrata are more appropriate to be divided into two varieties, although they are combined in the classical morphological classification. The intraspecific genetic relationship of different Sect. Thea(L.) Dyer is directly related to their geographical origin. Therefore, the same geographical source material hybrid application should be avoided in breeding practice.