AbstractGinkgo biloba , now unique in the Ginkgopsida, is referred as a “living fossil” plant. As a wild species, Ginkgo biloba is endemic to China. ISSR analysis was conducted on the possible natural populations (Tianmushan, Wuchuan, and Dahongshan) and the cultivated populations (Taixing and New York) in order to investigate the genetic diversity and the genetic structure of the populations. Out of 100 ISSR primers, 13 generated highly reproducible and stable DNA fragments. Using these primers, 88 discernible DNA fragments were produced. Of these, 62 (PPB = 70.5%) were polymorphic loci, which indicated that high levels of genetic variation existed in the possible natural populations. The result of POPGENE analysis indicated that the level of genetic variation of Ginkgo biloba ( H_e = 0.2408; H_o = 0.3599) was higher than other endangered or relict gymnosperms. The Wuchuan population possessed the highest level of genetic diversity(PPB = 56.82%, H_e= 0.2089, H_o = 0.3087),while the cultivated populations, Taixing(PPB = 34.09%, H_e= 0.1269, H_o= 0.1858) and New York(PPB= 23.86%, H_e = 0.0884, H_o= 0.1312), exhibited lower levels of genetic diversity than the possible natural populations (Tianmushan, Wuchuan and Dahongshan). Nei's genetic diversity analysis and analysis of molecular variance (AMOVA) showed that there was a certain level of genetic differentiation (G_st = 0.1476, Ф_st=14.26%) among the three possible natural populations. Some differentiation may be caused by human selective pressures and barriers to gene flow. The dendrograms of genetic relationships among populations and among individuals were constructed based on Nei's genetic distance. The Wuchuan and Tianmushan populations clustered in a clade. Close relationship was revealed between the New York and Dahongshan populations, which means that they are likely the offspring of the same natural population. The combined results of the analysis of population genetic structure and community investigation suggest that Wuchuan may be a natural population. Based on ecological and genetic information available for Ginkgo biloba , two management strategies are proposed. The first would consist of an in situ conservation plan that defines conservation areas free from significant disruption for the genetically most diverse population and the optimal habitat (namely Wuchuan). The second would be to cross-transplant adult plants or seedlings mutually among populations in order to enhance the gene flow. By this means, the genetic diversity resources of the species can be preserved to the greatest extent.