The transcriptional regulator XylR plays a pivotal role in coordinating carbohydrate metabolism and virulence in Xanthomonas species, a group of economically important plant pathogens. This study presents a comprehensive phylogenetic analysis of XylR across 50 Xanthomonas strains using neighbor-joining methods with 1000 bootstrap replicates. Our analysis revealed six well-supported clades (bootstrap ≥70%) that correlate strongly with host specificity and pathogenic lifestyle. Notably, rice pathogens X. oryzae pv. oryzae and oryzicola formed an exceptionally conserved cluster (99% bootstrap), while broad-host X. campestris strains showed moderate divergence. Intriguingly, X. arboricola pathovars exhibited polyphyletic distribution, suggesting either multiple horizontal gene transfer events or host-specific evolutionary pressures. The phylogenetic position of Pseudomonas amygdali as an outgroup (100% bootstrap) confirmed the genus-specific specialization of XylR. These evolutionary patterns suggest XylR maintains core metabolic functions while acquiring host-specific regulatory capabilities. Our findings provide new insights into Xanthomonas evolution and identify conserved regions of XylR as potential targets for developing broad-spectrum anti-virulence strategies. This work establishes a foundation for future functional studies of XylR alleles and their contributions to pathogenicity in different host systems.