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Virulence analysis and two polymerase chain reaction-based assays were used to evaluate the population structure of Xanthomonas oryzae pv . oryzae (Xoo) from different elevations ranging from 150 to 2600 m in south-west China. Among the 218 isolates of Xoo, 18 pathotypes were identified using six near-isogenic rice lines, each containing a single resistance gene. Among them, pathotype 9 predominated in low and mid-elevations was virulent to all resistance genes, including Xa2, Xa3, xa5, xa13, Xa14 and Xa18. However, pathotype 2 was predominant at high elevation and was virulent to Xa18 only. The 18 pathotypes were grouped into four clusters. Isolates belonging to cluster 1 were mainly found at high and mid-elevations, while those of cluster 4 were mainly found at low elevations. There were significant trends of virulence of isolates from low to high with the elevation from high to low. The ERIC and J3 primers were used to screen the genomes of 218 isolates, and 56 molecular haplotypes were found. Multiple correspondence analyses revealed that 56 haplotypes were divided into four putative genetic lineages. Lineage 2 was the most frequently detected from 150 to 2600 m; it was clearly shown that isolates from high elevation with 80% is much more than from low and mid-elevation in the lineage. It is intriguing that genetic variation of Xoo is restricted by physical geographical barriers of elevations. This is the first report on the relationship of pathotypic and genotypic diversity of Xoo at different elevations. [ABSTRACT FROM AUTHOR]