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Draft genome sequencing has become cost-effective and time saving with the advent of next generation sequencing methods. The increasing scale of genomics provides a rapid means for identifying virulence factors and for generating new hypotheses to explain the complexities of host-pathogen interactions. Comparative genomics has raised a number of questions as to how diverse species evolve to extend host range and as to the role of type III effectors and molecular mechanisms in driving the evolution of the pathogen. In Florida, the bacterial spot of tomato pathogen <i>Xanthomonas euvesicatoria</i> (<i>Xe</i>) was the only species associated with tomato. In 1991, <i>Xanthomonas perforans</i> (<i>Xp</i>) was identified and as of 2006 has become the predominant species in tomato fields. Until recently, only <i>Xe</i> has been pathogenic on pepper. AvrXv3 present in <i>Xp</i> strains restricted host range on pepper. We recently isolated and sequenced an <i>Xp</i> strain that is able to infect pepper. We also sequenced <i>Xp</i> strains representative of the four tomato growing regions in Florida. <i>In silico</i> analysis of the genes present in the new pepper <i>Xp</i> strain, but absent from the previously sequenced <i>Xp</i>91-118, revealed candidate virulence factors on pepper. Differences in effector suites have evolved in these closely related field strains. Phylogenetic analysis based on MLST and SNPs revealed diversity among these field strains and, when related to the geographical distribution, possible clues to their evolution.<p><p>Keywords: