The two‐component regulatory system PhoP‐PhoQ of Pseudomonas aeruginosa regulates resistance to cationic antimicrobial peptides, polymyxin B and aminoglycosides in response to low Mg²⁺ conditions. We have identified a second two‐component regulatory system, PmrA‐PmrB, that regulates resistance to polymyxin B and cationic antimicrobial peptides. This system responds to limiting Mg²⁺, and is affected by a phoQ, but not a phoP mutation. Inactivation of the pmrB sensor kinase and pmrA response regulator greatly decreased the expression of the operon encoding pmrA‐pmrB while expression of the response regulator pmrA in trans resulted in increased activation suggesting that the pmrA‐pmrB operon is autoregulated. Interposon mutants in pmrB, pmrA, or in an intergenic region upstream of pmrA‐pmrB exhibited two to 16‐fold increased susceptibility to polymyxin B and cationic antimicrobial peptides. The pmrA‐pmrB operon was also found to be activated by a number of cationic peptides including polymyxins B and E, cattle indolicidin and synthetic variants as well as LL‐37, a component of human innate immunity, whereas peptides with the lowest minimum inhibitory concentrations tended to be the weakest inducers. Additionally, we showed that the putative LPS modification operon, PA3552‐PA3559, was also induced by cationic peptides, but its expression was only partially dependent on the PmrA‐PmrB system. The discovery that the PmrA‐PmrB two‐component system regulates resistance to cationic peptides and that both it and the putative LPS modification system are induced by cationic antimicrobial peptides has major implications for the development of these antibiotics as a therapy for P. aeruginosa infections.