Bacterial plant pathogens secrete type III effectors (T3Es) to interact with and disrupt host cell defenses. Susceptibility or resistance of the host depends on their ability to recognize and restrict the establishment of the pathogen. Xanthomonas euvesicatoria (Xe) and X.perforans (Xp), causal agents of bacterial spot disease (BLS) on tomato and pepper, are informative models to study the roles of effectors in host-pathogen interactions. Xe infects tomato and pepper, Xp infects only tomato, however, Xp strains have been isolated from pepper. To understand factors that influence the presence and distribution of effectors between and within species, we sequenced and analyzed the effector profiles of 179 and 131 strains, collected in 13 countries over time (25 to 56 yrs) for Xp and Xe, respectively. Both pathogens are distributed worldwide and follow a classical gene-for-gene interaction defining pathogenicity and virulence with respect to their host. Consequently, host, year and geographic origin were expected to influence the effector profiles of strains, including effector presence and allelic state. The core and non-core effectors within and between Xp and Xe strains are described, expanding previous knowledge of their effector content. However, host, year and country of collection do not explain the variation in effector profiles suggesting migration and distribution of strains impacts the population structure more than local demographic processes.