We report the presence of the emerging plant pathogen ‘
Xanthomonas cannabis
’ in Australia through a comprehensive analysis of five historical isolates and all publicly available genomes of the species. Using comparative genomics, we characterized four isolates collected from
Zinnia
spp. and one from
Cucurbita pepo
. Our findings show that the
Zinnia
isolates form a distinct phylogroup with the pathotype strain of ‘
X. cannabis
’ pv.
zinniae
. This group possesses genes for the type 3 secretion system (T3SS) and effectors, a variety of genes unique within the species, and nine genomic islands associated with virulence and drug resistance. In contrast, the
C. pepo
isolate is genetically distinct and lacks the T3SS but contains its own genes unique within the species. Hypersensitivity response assays confirmed the pathogenic potential of all five isolates in black bean, eggplant, green bean, tomato, sunflower, zinnia and zucchini plants. These results highlight the genetic diversity and evolving threat of this pathogen in Australia, underscoring the critical need for ongoing biosecurity surveillance.