Plant pathogenic bacteria are among the major challenges in crop production, amplified by their continuous and rapid evolution and resulting in the emergence of virulent, competitive, and elusive plant pathogens. To further understand these bacteria, their interactions with host plants, and their responses to disease management, comprehensive methods are necessary. In recent years, phytobacteriology research has used population and comparative studies to quantify the diversity of plant pathogenic bacteria and their virulence mechanisms, including the effectors secreted from different protein secretion systems, phytohormones, or toxins that mediate their interactions with the hosts and/or competing microbes in the phyllosphere. Studies comparing strains over time, within and among geographic regions, and across phylogenetic trees has provided insights into scales of variation and changes in pathogens over time and in response to selection pressures. In this series of articles, population and comparative genomics were used to investigate plant pathogens representing diverse bacterial genera including Gram-negative bacteria composed of facultative anaerobes (i.e., Dickeya, Pantoea, and Pectobacterium) as well as obligate aerobes (i.e., Pseudomonas, Xanthomonas, and Xylella) as well as the Gram-positive genus, Clavibacter.