Citrus canker disease is one of the most important diseases of citrus trees, especially limes in the southern regions of Iran, and is caused by Xanthomonas citri subsp. citri. The assessment of genetic diversity and studying the population structure of this pathogen can be used in the production of resistant varieties, reduction of disease and to adopt disease management strategies and also ecological and epidemiological studies. In the present study, 15 strains of citrus canker bacteria, isolated from citrus orchards in Kohgiluyeh and Boyer-ahmad provinces and LMG 9322 strain, as reference strain were investigated. To study the genetic diversity of X. citri subsp. citri , ISSR (primers UBC-841, UBC-846 and UBC-888) and RAPD (primers A-01, A-03, A-16, OPR-02 and OPR-20) markers were used. Dendrogram of Xanthomonas citri subsp. citri based on the abundance of alleles amplified by RAPD and ISSR primers were mapped using the Nei 1983 similarity coefficient and UPGMA method using MEGA 4.0 software (Molecular Evolutionary Genetic Analysis). To ensure the stability of the branches in the tree, the bootstrap value was calculated with 1000 replications. Based on the electrophoresis patterns of the RAPD primers, the dendrogram divides the strains, into three main groups. In the first group, were eight strains of both pathotypes A and A*, and all strains of A* pathotype were classified in this group. The strains of pathotype A formed the second and third groups. The dendrogram based on the results of the ISSR primers classified the strains into three main groups. The resultant grouping was indicative of placement of strains A and A* in the same group and in all groups, both pathotypes A and A* were grouped together. The electrophoresis patterns of replicated fragments with RAPD primers for differentiation of citrus canker strains revealed a high specificity of RAPD-PCR in pathotype differentiation.