Xanthomonas perforans (Xp), causal agent of bacterial spot of tomato, uses type III secreted effectors to infect hosts. Phylogenetic comparisons have identified at least 3 distinct groups (designated 1-3) of Xp strains that vary in effector profile. We compared the effector repertoires among Xp strains and identified three xopQ alleles in which one was associated with group 2 Xp strains that were pathogenic on pepper. We also identified xopJ4 in all tomato strains, but not in an Xp strain, Xp2010, that was isolated from pepper and determined to be pathogenic on this host. Based on these observations we hypothesized that XopJ4 may be a negative factor for virulence in pepper, while the XopQ alleles, found in Xp2010 and other tomato strains that cause disease on pepper, is a positive factor in pepper pathogenicity. The xopJ4 gene was conjugated in Xp2010, and disrupted in representative tomato strains. Likewise, xopQ was disrupted in Xp strains representing different phylogenetic groups, including Xp2010. Strains were compared for bacterial growth in pepper leaves. Expression of XopJ4 in Xp2010 suppressed bacterial growth in pepper, whereas disruption of xopJ4 in tomato strains had no effect. Meanwhile, disrupting xopQ lowered bacterial growth only for group 2 Xp strains in pepper. Our results suggest that contribution of individual effectors towards overall pathogenicity depends on genetic background of strains.