Abstract: To evaluate the genetic diversity level and provide theoretical basis of ex-situ conservation populations of Cupressus chengiana,the genetic diversity,genetic structure,and gene flow of ex-situ conservation populations and wild populations of C.chengiana were studied respectively.The principal component analysis（PCA）,cluster analysis,construction of molecular evolutionary tree,genetic diversity and genetic structure of three wild populations and ex-situ conservation populations based on SNP locus were obtained respectively from Genotyping-by-Sequencing technology（GBS）sequencing.The results showed that high quality clean data 118 321 514 728 bp was obtained by GBS sequencing,and 1 947 047 tags were developed.After being screened,a total of 1 259 610 of high-quality SNP sites were retained.The valley value of cross validation error rate determined that the optimal number of clusters was 1.The phylogenetic tree indicated that most of individuals ex-situ conservation populations and wild populations were clustered together.Both of combined ex-situ conservation populations and wild populations of C.chengiana had higher genetic diversity,and their value of heterozygosity（H_o）,expected heterozygosity（H_e）,Shannon information index(S_hi),inbreeding coefficient(F_is),and percentage of polymorphic loci(P_ic)were 0.181 5-0.272 0,0.223 2-0.300 3,0.331 0-0.464 9,0.178 0-0.246 5 and 0.272 2-0.309 2,respectively.Genetic diversity of ex-situ conservation cultivated populations was relatively higher than the wild populations of C.chengiana,the value of H_eand S_hi was 0.300 3 and 0.464 9,respectively.The wild populations of C.chengiana of Baiwan tunnel（BW）＿vs＿Songgang town（SA）had the greater genetic differentiation and the gene flow（N_m）were lower than other populations(F_st=0.091,N_m=2.496).The results indicated that genetic differentiation had not occurred among these C.chengiana populations,and the gene had exchanges frequently among the ex-situ conservation populations and wild populations of C.chengiana(F_st＜0.05,N_m＞4).There was a close genetic relationship between the ex-situ conservation individuals and the wild populations individuals,and there was no obvious clustering phenomenon.Thus,transplanting endangered plants was a better method in ex-situ conservation.This paper would provide a reference for the ex-situ conservation populations of wild populations C.chengiana and provided a theoretical reference for the conservation of other tree germplasm resources.