Elaeagnus mollis Diels is an endemic and endangered tree in China.Twenty primer pairs were selected by the combined biotin capture and identified in two populations of E.mollis.Nineteen pairs showed highly polymorphic,and were selectively neutral and the locus CGY19 was monomorphic.One locus manifested significant deviation from Hardy-Weinberg Equilibrium (P<0.01),which was probably caused by the influence of selection.No significant linkage disequilibrium was detected among pairs of loci in each pair.With a mean of 4.225,the number of alleles per locus ranged from 1 to 9.The observed and expected heterozygosity (H_O and H_E) per locus ranged from 0 to 0.900 and from 0 to 0.847,respectively.The genetic diversity levels of 2 natural populations of E.mollis were estimated by these 19 pairs of SSR markers obtained in this study.It showed that the mean genetic diversity was 97.37%,indicating that the loss of genetic diversity was not the cause of the endangerment of E.mollis.The significant fragmentation (F_ST=0.033 1) was tested between the two populations and it provided the evidence that the genetic variation mainly existed in the populations.Furthermore,due to the frequent gene flow between populations (N_m=32.081 8),it also verified the Shannon’s information index (I=genetic similarity) was very high in each population.On a long view,the new set of loci and the information of genetic diversity will be applied in the mating system and population structure of this species and provide valuable information for its sampling strategy,conservation and utilization.