Abstract: Based on the specific agro-ecological system and vertical climate in Southwest China, two polymerase chain reaction- based assays (rep-PCR and IS-PCR) were used to evaluate the population structure of Xanthomonas oryzae pv. oryzae (Xoo) from different elevation ranges (150 to 2 600 m) in Southwest China, which belong to six climate zones - north tropical climate zone, south subtropical climate zone, central subtropical climate zone, north subtropical climate zone, south temperate climate zone and cold temperate zone. A total of 218 isolates were tested in the research, out of which 73 isolates were collected from low elevation range (150?1 200 m), 90 isolates from medium elevation range (1 200?1 800 m) and 55 isolates from high elevation range (1 800? 2 600 m). The genetic diversity of Xoo was high in Southwest China, a total of 56 haplotypes were identified. The Xoo haplotypes in different elevation ranges were different, of which 18 were tested in high elevation range, 28 in low elevation range and 34 in medium elevation range. Although genetic diversity of Xoo was high, only H10 and H39 of haplotypes were tested in all the three different elevation ranges. Significant differences in the genetic diversity (Shannon Wiener index) of Xoo were observed among different elevation ranges. According to t-test, Shannon Wiener index in low and medium elevation ranges was significantly higher (P < 0.05) than that in high elevation range. However, no significant difference (P > 0.05) existed between medium and low elevation ranges. The genetic diversity of Xoo gradually reduced with decreasing temperature in different climate zones. Basis on cluster analysis of UPGMA, the 56 haplotypes of Xoo strains constituted nine putative genetic lineages. While strains from low elevation occurred under lineage 1 and lineage 2, strains from medium and high elevations occurred under lineage 3 to lineage 6 and lineage 3 to lineage 5. There were visible differences in Xoo strains from different elevation ranges. It was therefore recommended to take into account genetic diversity and variation degree of Xoo when laying out resistant genes based on haplotypes. This could slow down the rate of variability of Xoo strains on host selection pressure and avoid rapid lose of rice resistance.