Xanthomonas perforans (Xp) and X. euvesicatoria (Xe) cause bacterial spot disease (BLS) on tomato and pepper. Symptoms include necrotic lesions on leaves, sepals, and fruits, incurring major crop yield and economic losses worldwide. Xp and Xe have high genome plasticity and recent findings demonstrate a high rate of recombination among them. Xp, which was historically restricted to tomato, has recently been found causing bacterial spot of pepper. The complex host-pathogen interactions of BLS Xanthomonas, known to depend largely on type III effectors (T3E), are not yet fully understood. The content and distribution of T3E were analyzed in a worldwide sample of 269 Xp and 131 Xe strains. The influence of demographic processes, such as geographic location, host and year of collection, on the structure of the effector profiles were examined. Using this broad sample, core and non-core effectors common and unique to each species are described, expanding current knowledge. This is a first step towards identifying the complex demographic processes influencing the distribution of the effectors, hence, the evolution of host range and virulence in BLS strains.