Abstract: Glyptostrobus pensilis is a rare and endangered relict species in China. To make a comparative study on the genetic diversity and genetic structure of
 natural and planted G. pensilis populations would have significance in the conservation and proliferation of the species. Samples from the main distribution regions of G. pensilis were analyzed by ISSR (inter simple sequence repeats) molecular marker. A total of 95 discernible DNA fragments were detected with 10 ISSR primers, of which, polymorphic loci occupied 39.0%, suggesting that the genetic variation in the test G. pensilis populations was at a very low level,compared with other endangered gymnosperm．The genetic differential index (G_st=0.3982) and the gene flow (N_m=0.3778) indicated that there existed genetic differentiation among populations but the differentiation dominated within populations. There was a significant positive correlation between genetic distance and geographical distance. The mean values of polymorphic loci (P), Nei’s gene index (H_e), and Shannon information index (I) of natural populations (P=39.9%, H_e=0.1499, I=0.2202) were much higher than those of planted G. pensilis populations (P=30.7%, H_e=0.1265, I=0.1759), and the coefficient of gene differentiation (G_st) and genetic distance (D) of natural populations (G_st=0.4513, D=0.0301) were also much higher than those of the planted populations (G_st=0.3025, D=0.0192).

Key words: Glyptostrobus pensilis, genetic diversity, genetic structure, natural population, planted population, ISSR, spatial distribution, diameter distribution, secondary forest, scale effect