Abstract:The genetic relationships among 26 cultivars of Camellia japonica were analyzed by inter-simple sequence repeat (ISSR) molecular-marked technique. Fourteen ISSR primers were screened to assess the genomes of 26 cultivars of C.japonica. The results showed that a total of 166 DNA bands were amplified and 140 of which (84.34%) were polymorphic. The Nei-Li genetic similarity was 0.708, UPGMA method cluster analysis indicated that these 26 cultivars were classified into 5 cluster groups, and they were classified into 10 subcluster groups with the genetic similarity of 0.726. The Nei-Li genetic similarities of 26 cultivars ranged from 0.615 to 0.913, with average value of 0.704, suggesting that the genetic differences among the 26 cultivars were relatively little. The genetic similarity coefficient between Mudancha and Huamudan was 0.913, showed that Mudancha maybe the bud mutant variety of Huamudan. The ancient Camellia trees are precious resources, management strategies should be proposed to prevent the loss of the ancient tree resources.