Abstract: Genetic diversity of 248 individuals from 12 natural populations of Rubus delavayi Fanch.，which are specific but endangered species in Yunnan，was assessed using ISSR markers. The results showed that 199 amplified bands were got in PCR when sixteen primers were used. Among those bands，185（92.96% of the total bands）were polymorphic. A high level of genetic diversity was showed in these populations. At species level，percentage of polymorphic loci（PPB）was 97.99%，effective number of alleles（A_e）was 1.427，Nei’s gene diversity（H）was 0.267，and Shannon’s information index（I）was 0.417. At population level，PPB was 62.10%，A_e was 1.289，H was 0.177，I was 0.275. The level of genetic differentiation between populations was lower than that within populations. The coefficient of gene differentiation（G_st）betweenthe populations was 0.3351. And the gene differentiation contributed to 33.51% of the total genetic variations between the populations and to 66.49% within the populations. The total gene flow（N_m）was 0.9923. There was no significant correlation between genetic and geographic distances among population（r = 0.0286，P = 0.5240）in the Mantel test. The result of UPGMA clustering analysis was basically similar to that of the principle coordinate analysis（PCA）. The high genetic variation level within populations could be caused mainly by the significant genetic variation inside a population together with the limited gene flow（N_m = 0.9923）between populations. While the lower genetic diversity among the populations could be caused by severely destroyed and biological invasion of Eupatorium adenophorum Spreng.

Key words: Rubus delavayi, ISSR, genetic diversity, genetic differentiation