The emergence and spread of various multidrug-resistant bacterial strains have posed alarming challenges to public health and agriculture worldwide. Public demand for new antibiotics is enormous, yet drug development pipelines of the pharmaceutical industry started to run dry with limited targets available for inventing new bactericidal antibiotics. It is important to uncover potential therapeutic targets. Our lab has been working on virulence regulation in the human pathogen Pseudomonas aeruginosa and plant pathogen Pseudomonas syringae, which are of world-wide importance. These pathogens rely on quorum sensing (QS) systems and type III secretion system (T3SS) to invade their hosts, which is finely regulated by a group of transcription factors (TF), two-component systems (TCS, ‘bacterial nervous system’) and signaling pathways. Research in our group has led to the identification of a variety of new virulence factors and their molecular mechanisms. Specifically, we have characterized the signal cascade of RhpRS-hrpR-T3SS, that is targeted by host polyphenols. We also found that RNA epigenetic marks (such as m6A and rG4) play important roles in regulating bacteria virulence. We have mapped the complicated TF-based regulatory networks for both superbugs, which identify a group of master virulence regulators. Tuning their expression and developing inhibitors are key for the development of strategies to control Pseudomonas infections.