Abstract: We used ISSR molecular markers to study the genetic structure of 21 Cymbidium goeringii (Rchb. f.) Rchb. f. populations in the main mountain range of Jiangxi Province, China. Results showed that 139 bands were amplified by the 14 selected primers. Among these bands, 118 were polymorphic, resulting in a percentage of polymorphic bands (PPL) of 84.89%. The Nei’s gene diversity (He) and Shannon index (I) values of the 21 populations were 0.2292 and 0.3613, respectively. AMOVA analysis unveiled that inter-population variation (50.79%) was greater than intra-population variation (49.21%). Both these results of population genetic structure and UPGMA cluster analysis showed that the C. goeringii populations in the main mountain range of Jiangxi Province were geographically isolated and their habitats were fragmented. Based on the above analysis, we inferred that C. goeringii was once widely distributed in the mountain ranges of Luoxiao and Wuyi. Following the Quaternary glacial period, these populations declined sharply due to severe climate change, but were preserved to the present day in suitable environments between these two mountains. Thus, the Luoxiao and Wuyi mountains formed primary ice-age refuges for C. goeringii. These results, combined with the genetic diversity and structure of C. goeringii populations, may provide a valuable basis for conservation strategies. In situ conservation would be suitable for the Shicheng (SC), Yifeng (YF), and Guixi (GX) populations due to their sufficient genetic diversity, whereas ex situ strategies should be considered for Dayu (DY) and Jinggangshan (JGS), which have experienced serious resource destruction.