Abstract:Genetic diversity and genetic structure of five Reaumuria trigyna populations was analyzed by ISSR(inter simple sequence repeat) markers. Using 14 primers，114 loci were observed，among them 99 were polymorphic.The proportion of polymorphic loci was 86.84%. R.trigyna was the higher genetic diversity than other endangered shrubs. At species level，Shannon index(I) was 0.468 8，Nei’s gene diversity index(H) was 0.308 4. The proportion of polymorphic loci was 77.89%，I=0.410 6，H=0.260 9 respectively at population level. The coefficient of gene differentiation(Gst=0.106 9) showed that there were more genetic variations within the population than among populations，genetic differentiation among populations were 10.69%. Gene flow(Nm) was 4.178 7＞1，showed that gene interflow were among populations，genetic differentiation were prevented due to genetic drift. Cluster analysis showed that there was no direct correlation between genetic distance and geographic distance. The results indicated that genetic diversity was related to species traits and community. The endangered plants was not certainly displayed lower level of genetic variation.