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Copper‐based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid‐encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite‐based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper‐resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper‐resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper‐resistant Xanthomonas and …