Abstract:240 samples of Camellia japonica collected from 8 populations in Zhejiang Province and Qingdao City of Shangdong Province were analyzed by inter-simple sequence repeat (ISSR) markers to detect their genetic structure. 210 discernible loci were obtained from all the populations using 20 primers. Of these loci, 87.62% was polymorphic (PPB=87.62%). The average percentage of polymorphic loci (PPB=68.99%), Nei’s gene diversity (HE=0.256 9) and Shannon’s Information Index (H=0.377 9), estimated by POPGENE1.32, indicated that the C. japonica had higher level genetic diversity than many other insular plant species. The coefficient gene differentiation (Gst) was 0.182 9, indicating more variation was from the individuals of the populations. According to Mantel Test (r = 0.856 7,P< 0.05), geographical isolation had an important influence on genetic structure. UPGMA analysis revealed that there was a close relationship among 5 populations, the two populations from Qingdao might be translocated from Changmenyan Island. In order to maintain the genetic diversity and promote the resource utilization, the C. japonica natural population should be protected in situ and facilitate its natural generation.