Objective To compare the periodontal indices and Porphyromonas gingivalis(P. gingivalis) between the use of self-ligating brackets and conventional brackets.Methods Thirty patients were divided into 2 groups(n=15). Self-ligating brackets were used in the experimental group. Conventional brackets were used in the control group. Cli-nical periodontal indices, including plaque index(PLI), gingival index(GI) and probing depth(PD) of observed teeth were examined at three different time points: Before orthodontic treatment, the first month after treatment and the third month after treatment. Subgingival plaques were collected simultaneously at each time point. The number of total bac-teria and P. gingivalis in each sample were detectd and quantitated by real-time quantitative polymerase chain reaction, the percentage of P. gingivalis in total bacteria was obtained.Results Before treatment, the periodontal indices and the percentage of P. gingivalis in total bacteria had no difference between the two groups(P>0.05). After 1 and 3 months respectively, the periodontal indices and the percentage of P. gingivalis in total bacteria increased with time(P<0.05) and were obviously lower than those of the control group(P<0.05).Conclusion Compared with conventional brackets, the self-ligating brackets are better for periodontal health. But it is adverse effect on oral health.