ISSR markers were used to study the genetic diversity, genetic structure and genetic distance of three populations of Pinus massoniana from Guangxi Zhuang Autonomous Region and Guizhou provinces. Of the 100 primers screened,12 primers were selected and they generated 92 stable bands, among which 86 bands were polymorphic. The result of POPGENE indicated that Nei' s gene diversities(h)at population level were from 0.182 4 to 0.206 5, Shannon's information indexes(I)at population level were from 0.281 8 to 0.317 8, which suggested that the polymorphism level of three populations had small differences. At species level, the percentage of polymorphic bands(PPB)were 93.48%, Nei's gene diversities(H)was 0. 284 2, Shannon's information index(I)was 0.438 1. All those showed that P. massoniana had a higher genetic diversity at the species level. The analysis of genetic structure indicated that the average coefficient gene differentiation(Gst)was 0.315 3, which implied most of genetic variation appeared inner population. And the average number of the gene flow was 1.085 3, which indicated that there were a certain degree of gene exchanges between each population of P. massoniana. The result of AMOVA showed that the genetic differentiation index was 0.246(P=0.001), which indicated that the genetic differentiation was evident among different populations although there were gene exchanges between them. The UPGMA clustering and Mantel test showed that every individual inner population was first gathered for a branch. And there was significant correlation between the genetic distance and geographical distance among these three populations(r=0.972, P=0.001). Therefore, it was concluded from above that the P. massoniana was at a higher level of genetic diversity in gymnosperms; and the majority of genetic variation distributed within population; and the genetic differentiation from different populations of P. massoniana was hardly associated with the genetic drift but maybe caused by the difference from geographical and ecological environments. This study will provide theoretical reference and scientific basis for genetic improvement and plant introduction of P. massoniana. [ABSTRACT FROM AUTHOR]