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12 ISSR primers and ITS primer were used to ISSR and ITS molecular marker analysis within 17 Cymbidiumfaberi Rolfe wild populations mainly distributed in Jiangxi and Fujian.ISSR results indicated that the genetic diversity of C.faberi Rolfe at the species level (PPF=90.85%,Hpop=0.2892,I=0.4393) and at the population level (PPF=59.40%,Hpop=0.1886,I=0.2865) were relatively high.It showed that the genetic differentiation within population was greater than the one among populations and the genetic differentiation among populations was weaker than the one within populations separately located in five Mountains was.Mantel statistics and analysis of genetic distance and geographical distance of seventeen C.faberi Rolfe populations showed that correlation between geographical isolation and genetic differentiation was unobvious.The length of the entire ITS region in C.faberi Rolfe ranges from 654 to 659bp,G+C content range from 54.17% to 69.01%.ITS sequences have 178 variable sites,126parsimony informative sites.A total of 11 kinds of ITS types were showed in 17wild populations 170 samples of Jiangxi Province,ITS type of Mufu Mountains was single,both Huaiyu Mountains and Jiuling Mountains contain three kinds of ITS types,the Luoxiao and Wuyi Mountains respectively contain 5 and 6 ITS types,Jiangxi C.faberi Rolfe intraspecific show high level of genetic diversity