Genetic structure and genetic diversity 252 individuals in 17 natural populations of Cymbidium kanran distributed in Jiangxi Province were studied by using chloroplast genome fragment (petbpetd) and nuclear genome ITS sequence. It provide some suggestions for the analysis of the reason of the decrease in the number of wild C. kanran in Jiangxi Province and the protection and rational utilization of wild cold orchid resources. The results showed that： (1) there were a total of 652-658 bp of nrDNA ITS sequences, with 140 variable loci, the percentage of variation loci was 21.3% to 21.5%, and the content of (G+C) was 58.9% to 67.1%. The sequence length of cpDNA was 522-529 bp, with 9 variable loci, the percentage of mutation sites was 1.70%-1.72%, and the content of (G+C) was 32.9% to 33.7%. (2) Molecular analysis of variance (AMOVA) showed that the genetic variation within populations was greater than that between populations, the genetic variation of cpDNA was 40.76% among population and 59.24% within population the genetic variation of ITS was 28.96% among population and 71.04% within population; While gene flow was high, cpDNA: N_m=1.226 5; ITS: N_m=0.726 7. (3) Through the mismatch analysis of ITS and cpDNA data, it is shown that the wild population of Cymbidium kanran Makino has experienced an expansion event recently. ITS sequence of nrDNA evolved faster and mutated faster than chloroplast DNA sequence.