The growth responses of Phellodendron amurense root-derived materials against seven intestinal bacteria were examined, using an impregnated paper disk agar diffusion method and spectrometric method under $O_2$-free condition. The biologically active constituent of the P. amurense root extract was characterized as berberine chloride ($C_{20}H_{18}NO_{41}Cl$) using various spectroscopic analyses. The growth responses varied depending on the bacterial strain, chemicals, and dose tested. At 1 mg/disk, berberine chloride strongly inhibited the growth of Clostridium perfringens, and moderately inhibited the growth of Escherichia coli and Streptococcus mutans without any adverse effects on the growth of three lactic acid-bacteria (Bifidobacterium bifidum, B. longum, and Lactobacillus acidophilus). The structure-activity relationship revealed that berberine chloride exhibited more growth-inhibiting activity against C. perfringens, E. coli, and S. mutans than berberine iodide and berberine sulfate. These results, therefore, indicate that the growth-inhibiting activity of the three berberines was much more pronounced as chloridated analogue than iodided and sulphated analogues. As for the morphological effect caused by 1 mg/disk of berberine chloride, most strains of C. perfringens were damaged and killed, indicating that berberine chloride showed a strong inhibition against C. perfringens. As naturally occurring growth-inhibiting agents, the P. amurense root-derived materials described could be useful as a preventive agent against diseases caused by harmful intestinal bacteria such as clostridia.