Multilocus sequence analysis for xanthomonads indicated a very close relationship between Xanthomonas gardneri, a tomato and pepper pathogen, and Xanthomonas cynarae, an artichoke pathogen. Whole-genome comparisons of representative strains from the two species revealed that the average nucleotide identity between the two species was above the threshold of 95-96%, and the two species could be merged into a single species. The type-III secretion systems of the two species were nearly identical, with minor differences in two genes. Furthermore, comparison of the type-III effector profiles showed high similarity. Given the close relationship between the species, we speculated that the two organisms might cross-infect. Inoculation of X. gardneri into artichoke resulted in a moderate disease reaction, although the disease on the bracts was very weak. Furthermore, following infiltration of leaves, X. cynarae reached significantly higher internal populations than X. gardneri. Infiltration of both species into pepper showed that the two species grew equally well and caused typical bacterial spot lesions. However, infiltration of X. cynarae at high concentration into tomato leaflets resulted in a hypersensitive reaction (HR). We have identified a unique gene associated with this HR and created a deletion mutant of this gene to determine whether this is the host-limiting factor. The mutant strain elicited an HR, indicating the presence of at least one additional factor in X. cynarae that limits its ability to colonize tomato.