Objective To study the antibacterial mechanisms of berberine and try to understand the reasons why bacteria cells difficultly resisted to it. Methods Detecting the minimal inhibitory concentration (MIC) of bacterial cultures incubated under sub-MIC concentration of berberine, Huanglian, and Neomycin for more than 200 generations, in order to analyze the bacteria resistance. Detecting the binding kinetics of berberine to DNA, RNA, and proteins. Observing the changes in bacterial cell surface structure with scanning electron microscopy. Detecting the Ca2+ and K+ released from berberine-treated bacterial cells with atomic absorption spectrum. Detection the absorption of methyl-3H-thymine (3H-dT), 3H-uridine (3H-U), and 3H-tyrosine (3H-Tyr) into berberine-treated bacterial cells. Results MICs of bacterial cultures, growing more than 200 generations in MH medium with 1/2 MIC of berberine (BA200) or Huanglian (HA200), did not increase compared to the control, while remarkably increased in MH medium with 1/2 MIC of Neomycin (NA200). In addition, from the culture NA200 it was easy to isolate resistant mutant strains which could grow in MH medium with more than four times MIC Neomycin, but from the culture BA200 and HA200 it was difficult to isolate berberine or Huanglian mutant strains could grow in MH medium with more than four times MIC berberine or Huanglian. The binding kinetics of berberine to DNA, RNA, and proteins illustrated that berberine could easily and tightly bind to DNA and RNA, and hardly dis-bind from DNA- and RNA-berberine complexes. Berberine could easily bind to protein too, but also easily dis-bind from berberine-protein complex. The bacterial cells treated with berberine sharply decreased the absorption of 3H-dT, 3H-U, and 3H-Tyr, as the radioactive precursors of DNA, RNA, and protein biosynthesis. Berberine could damage bacterial cell surface structure, especially for Gram-negative bacteria. Ca2+ and K+ released from berberine-treated cells increased significantly compared to the control. Conclusion All of above results indicate that bacterial cells could not easily become resistant mutants to berberine. The mechanisms for the bactericidal effect of berberine include: inhibiting DNA duplication, RNA transcription, and protein biosynthesis; influencing or inhibiting enzyme activities; destructing the bacterial cell surface structure and resulting in Ca2+ and K+ released from cells. All of the berberine bactericidal mechanisms are the most essential physiological functions for a live cell, if influenced any one such function, the mutation would be lethal mutation, so that it is difficult to get berberine resistant cells. The results in this paper also prefigure that berberine and its related Chinese medicines would provide a feasible way to control antibiotic resistance problem.