In order to reveal the cause of disease occurred in the process of Coptis chinensis growth, this paper studied the bacterial species diversity index of different aged rhizospheric and non-rhizospheric soil planting normal or sick C. chinensis by using PCR-DGGE technique. The representative DGGE bands were chosen to be cloned, and sequenced, the phylogeny were constructed. The results showed that the bacterial communities were very different between the normal and diseased soil samples of C. chinensis, and the diversity index (H) of diseased soil samples were higher than that of normal soil samples. Sequencing analysis of representative cloned DGGE bands showed that the unculturable bacteria were the dominant groups, and bacteria belonged to genus Bacillus, Acidovorax, Acinetobacter, uncultured Kluyvera, and uncultured Comamonas were also existing, but the reported plant pathogenic bacteria were not found in the C. chinensis planting soil. The density and brightness of clone band d in diseased soil samples was higher than that in normal soil sample, and sequencing analysis showed that it belonged to genus Acidovorax. Obviously, during the process of C. chinensis growth, the rhizospheric bacteria population changed, and the quantity of bacteria belong Acidovorax increased, which probably resulted in the disease occurred during C. chinensis growth.