Abstract:Random amplified polymorphic DNA (RAPD) markers were used to estimate the genetic diversity and population genetic differentiation in eight natural populations of Phoebe bournei from Jiangxi and Fujian provinces, China. In the 160 individuals, 12 random primers generated a total of 135 reproducible and discernible loci, among which 134 were polymorphic. 37.3% of genetic variance was observed among populations, as revealed by POPGENE software after Lynch & Milligan′s (1994) correction. And according to the analysis of Shannon′ index of phenotypic diversity, 46.4% of genetic variation resided among populations. This was congruent with estimation of genetic variation by the analysis of molecular variance (AMOVA), which revealed that 43.3% of the total genetic diversity (P<0.001) was found among populations. Although its genetic variation mainly existed within populations, strong genetic differentiation occurred among populations perhaps mainly due to habitat fragmentation and isolation by distance, these were also the main causes for its endangered situation. Based on the results presented in this study, we recommended that attentions should be paid to protect as more populations as possible of this species, especially those populations with high genetic diversity in Xiqin, Pucheng and Mingxi, Fujian Province, and to collect genetic resources in the whole distribution areas for ex-situ conservation. It is also essential to enlarge its population scale by breeding and increase gene flow carefully by proper return-to-nature methods, so as to maintain its high level of genetic diversity.