Population biology has the ability to refine our understanding of the biology of plant pathogenic xanthomonads, which remains partial despite the major significance of some of them as agricultural threats. We developed direct microsatellite genotyping from canker lesions caused by Xanthomonas citri pv. citri and applied it to investigate the genetic and spatial structure of the pathogen at several microgeographic scales in a situation of disease endemicity. This approach allowed identifying outbreaks with multiple inoculum sources and comparing genetic lineages in terms of transmission ability. ln a citrus grove where copper-susceptible and copper-resistant strains co-existed, our results suggested a range of spatial dependencyfourtimes largerforthe latter ones. Aggregated spatial patterns estimated from genotyping data were consistent with that previously determined from disease severity data in Argentina. How RST outperformed FST for differentiation analyses was scale-dependent. Linkage disequilibrium was maintained at smalt scales, likely as a confounding consequence of clonality and admixture. Finally, our results highlighted in ca. 1 % of samples a within-lesion polymorphism that likely reflects polyclonal infections. Because of their major biological significance as an inoculum source, we suggest that cankers may represent a preferred niche for horizontal gene transfer.