SSR primers were developed by using the magnetic bead enrichment method in Cymbidium faberi, and the polymorphic primers were used as research tools to explore the relationship between the genetic diversity and the geographical distribution for nine selected wild populations of Cymbidium from the Chongqing-Guizhou-Sichuan Region in China. The results showed that a total of 53 alleles were amplified by 8 pairs of SSR primers. The average number of alleles per locus was 6.625, and the average percentage of polymorphic fragments (PPF) was 98.6%. Mating imbalance between individual plants of Cymbidium was detected. The range of Nei’s diversity index (H) was 0.3158-0.8661, and the range of Shannon information diversity index (I) was 0.8833-1.3557. The genetic diversity of the Qianjiang populations in Chongqing was the highest, with 79.97% of the genetic differentiation within the population,and 20.03% of the genetic differentiation between the populations, the variation within the population being higher than that between the local populations. The gene flow of Nm<1 indicated that the genetic drift played some role in the genetic differentiation of the Cymbidium. By comparing the relationship between genetic clustering results among the populations and the geographic locations of the Cymbidium plants, it was found that the division of wild Cymbidium populations is greatly affected by geographic factors at the molecular genetic level.