The aim of this study was to characterize the physiological and molecular changes of Salmonella Typhimurium and Listeria monocytogenes in deionized water (DIW) and nisin solutions (100 IU/g) during high pressure processing (HPP). Strains of Salmonella Typhimurium and L. monocytogenes in DIW or nisin solutions were subjected to 200, 300, and 400 MPa for 20 min. The Weibull model adequately described the HPP inactivation of Salmonella Typhimurium and L. monocytogenes. Salmonella Typhimurium and L. monocytogenes populations were reduced to less than 1 CFU/ml in DIW and nisin solutions under 400 MPa. The highest b value was 5.75 for Salmonella Typhimurium in nisin solution under 400 MPa. L. monocytogenes was more sensitive to pressure change when suspended in DIW than when suspended in nisin. The pressure sensitivity of both Salmonella Typhimurium and L. monocytogenes was higher in DIW solution (141 to 243 MPa) than in nisin solution (608 to 872 MPa). No recovery of HPP-injured cells in DIW and nisin solutions treated at 400 MPa was observed after 7 days of refrigerated storage. The heterogeneity of HPP-treated cells was revealed in flow cytometry dot plots. The transcripts of stn, invA, prfA, and inlA were relatively down-regulated in HPP-treated nisin solution. The combination of high pressure and nisin could noticeably suppress the expression of virulence-associated genes. These results provide useful information for understanding the physiological and molecular characteristics of foodborne pathogens under high-pressure stress.