Twenty-six citrus leaf, branch or fruit samples showing typical symptoms caused by Xanthomonas citri subsp. citri (Xcc) were collected from six citrus producing areas in Hunan Province, and the citrus canker pathogen strains were isolated. Genomic polymorphisms among 12 geographically representative pathogen strains were analyzed by bacterial conserved 16S rDNA sequence analysis and repetitive sequence PCR gene fingerprinting (Rep-PCR) methods using citrus canker-specific primer. The results showed that the 12 strains showed the same number of polymorphic bands in BOX-PCR and ERIC-PCR and could not be distinguished by Rep-PCR, while tandem repeat polymorphism analysis showed that 3 strains, strain CCB-2, strain CCB-3 and strain CCB-10, showed fragment size polymorphism at the GT1 locus. Twelve strains of citrus canker were inoculated by in vivo injection into the leaves of ‘Bingtang’ sweet orange and two strains, strain CCB-2 and strain CCB-4, showed stable pathogenicity with a combined disease index of over 75%, indicating that strain CCB-2 may have polymorphism at the genomic sequence level compared to the other 11 strains and affect the pathogenicity level of the strain.