The complete genome sequence of *Xylella fastidiosa* clone 9a5c, which causes citrus variegated chlorosis (CVC), a serious disease of orange trees, has been reported. The genome consists of a 2,679,305-base-pair circular chromosome with a high GC content (52.7%) and two plasmids. About 47% of the 2,904 predicted coding regions have assigned functions, with efficient metabolic capabilities, primarily using sugars as energy and carbon sources. Pathogenicity mechanisms involve toxins, antibiotics, ion sequestration systems, and interactions between bacteria and hosts. Some proteins are unique to animal and human pathogens, indicating conserved and independent molecular bases for bacterial pathogenicity. At least 83 genes are bacteriophage-derived, including virulence-associated genes from other bacteria, providing evidence of phage-mediated horizontal gene transfer. The genome also encodes a variety of transport proteins, adhesins, and toxins, contributing to the bacterium's ability to colonize and cause disease in plants. The absence of avirulence genes suggests that insect-mediated transmission and vascular restriction are key to its host specificity. This study provides insights into the molecular mechanisms of *Xylella fastidiosa* pathogenicity and opens avenues for further research on control strategies for CVC.The complete genome sequence of *Xylella fastidiosa* clone 9a5c, which causes citrus variegated chlorosis (CVC), a serious disease of orange trees, has been reported. The genome consists of a 2,679,305-base-pair circular chromosome with a high GC content (52.7%) and two plasmids. About 47% of the 2,904 predicted coding regions have assigned functions, with efficient metabolic capabilities, primarily using sugars as energy and carbon sources. Pathogenicity mechanisms involve toxins, antibiotics, ion sequestration systems, and interactions between bacteria and hosts. Some proteins are unique to animal and human pathogens, indicating conserved and independent molecular bases for bacterial pathogenicity. At least 83 genes are bacteriophage-derived, including virulence-associated genes from other bacteria, providing evidence of phage-mediated horizontal gene transfer. The genome also encodes a variety of transport proteins, adhesins, and toxins, contributing to the bacterium's ability to colonize and cause disease in plants. The absence of avirulence genes suggests that insect-mediated transmission and vascular restriction are key to its host specificity. This study provides insights into the molecular mechanisms of *Xylella fastidiosa* pathogenicity and opens avenues for further research on control strategies for CVC.