The role of several multidrug resistance (MDR) systems in the pathogenicity of Erwinia chrysanthemi 3937 was analyzed. Using the blast algorithm, we have identified several MDR systems in the E. chrysanthemi genome and selected two acridine resistance (Acr)-like systems, two Emr-like systems, and one member of the major facilitator super-family family to characterize. We generated mutants in genes encoding for these systems and analyzed the virulence of the mutant strains in different hosts and their susceptibility to antibiotics, detergents, dyes, and plant compounds. We have observed that the mutant strains are differentially affected in their virulence in different hosts and that the susceptibility to toxic substances is also differential. Both Acr systems seem to be implicated in the resistance to the plant antimicrobial peptide thionin. Similarly, the emr1AB mutant is unable to grow in the presence of the potato protein tuber extract and shows a decreased virulence in this tissue. These results indicate that the function of these systems in plants could be related to the specificity to extrude a toxic compound that is present in a given host.