Abstract: Genetic diversity and structure of 11 Arundo donax populations (about 89 individuals in total) from 6 provinces were analysed with ISSR (inter simple sequence repeat) markers. From UBC 801-900, seven efficient ISSR primers were screened and a total of 40 loci were detected of which 38 were polymorphic. The length of PCR products ranged from 100 to 2 000 bp. At the species level, the Shannon index (I) was 0.494, Nei’s gene diversity index (H) was 0.329, the coefficient of genetic differentiation (G_st)was 0.826, and the gene flow (N_m) was 0.097. but the average genetic diversity within populations (H_s) was only 0.040. This showed that the gene diversity of A. donax was high at the species level but very low within populations. UPGMA clustering results showed that the 11 populations of A. donax could be divided into three groups: the populations from Zhejiang and Jiangsu clustered into one group, the populations from Hunan, Guizhou and Guangxi clustered into a second group, and the Yunnan population into a separate, third, distinct group. There was therefore some correlation between genetic distance and geographic distance, but it was not absolute.