Abstract: Genetic diversity and genetic differentiation of Torreya jackii Chun, an endemic species in China, were analyzed using Inter Simple Sequence Repeat(ISSR) molecular technique.Using 10 primers, ISSR amplification was conducted in 100 individuals from five populations collected in Xianju County, Zhejiang Province and 72 polymorphic loci were detected from total 136 loci.The total percentage of polymorphic loci(P) was 52.97%.Shannon's information index(I) and Nei's gene diversity(h) of T.jackii at species level was 0.269 1 and 0.175 8.It indicated that the genetic diversity at species level of T.jackii was relatively high, while at population level was relatively low.The means of P, I and h were 28.09%, (0.138 9) and 0.091 2 respectively.Analysis of molecular variance(AMOVA) demonstrated that the genetic differentiation among T.jackii populations was relatively high.The among-population component accounts for 45.72% of the total variation, while the within-population component acounts for 54.28%.The genetic differentiation coefficient(Gst) among populations was 0.489 1 and the gene flow among populations was low down to 0.522 4.It indicated that the bottle neck effect, population isolation and genetic drift might play main effects on the formation of low genetic diversity within populations and relative high genetic differentiation among populations.The mean genetic distance between every two populations was 0.128 0.Based on the geographic locations, these five populations could be clustered into two groups using unweighted pair group method arithmetic average(UPGMA), ie Xialiao(XL) populations and Longtankeng(LTK) populations were clustered into one group, and Shishe(SS) populations and Shichangkeng(SCK) populations were culstered first and then were clustered into another group with Jiafenkeng(JFK) populations.