Abstract: Fifty-six strains of Xanthomonas oryzae pv. oryzae (Xoo) were analysed by using short bacterial repetitive elements(REP,ERIC and BOX primers) and the repetitive DNA element IS1113 from X. oryzae pv.oryzae. Dendrograms were generated from the combination data sets of primers ERIC and J3 by using UPGMA analysis. The results indicated that extensive genetic variability and genetic diversity existed within the population of X. oryzae pv. oryzae strains tested. All strains could be divided into 10 groups at level of 70% similarity. Group 4, 5, 8, 9 and 10 were predominant. Strains collected from Yunnan Province were divided into 6 groups, and each group was partially associated with the regional origin of pathogen population. Eighteen pathotypes (virulence phenotype) were identified bg using 16 near-iso-genic rice lines, each containing a single gene for resistance. The pathotype diversity and complicity of strains tested from Yunnan Province were higher than those from other provinces in China. The results would be facilitated for further understanding of the population structure of X.oryzae pv.oryzae in China.