Abstract: Genetic diversities for five populations of Tilia miqueliana in China were studied by using ISSR marker. Eighty loci were generated with 11 simple sequence repeat primers screening from 55 primers, out of them, 76 were polymorphic and the percentage of polymorphic bands was 95.00%; with each primers amplified 7.0 bands on average. Shannon’s indices of diversity was 0.407 7 among the species level with the range of 0.211 7—0.322 7 among populations; Nei’s gene diversity was 0.264 3 among the species with the range of 0.140 5—0.211 9 among populations; the effective number of alleles was 1.432 6 among the species with the range of 1.240 3—1.356 6 among populations. The genetic variation among individuals was 65.01%, which was about twice of that among populations (34.99%) by AMOVA. The results revealed that variation among individuals was dominant. Genetic variance analysis showed that the gene diversity of species and gene diversity within populations were 0.257 1 and 0.176 0. The coefficient of gene differentiation was 0.315 4 at species level，and the gene flow was 1.085 5. The results consisted with that of AMOVA.Cluster analysis indicated that five populations could be divided into three groups. The results provided molecular data for the reasonable exploitation, utilization and molecular ecology of T.miqueliana resources.