Abstract: Objective： The purpose of this study is to find out the oral microbial community in healthy volunteers by meta-genomic method, and to provide the biological basis for the prognosis and consequences of the treatment of chronic periodontitis. Methods： Total DNA was extracted from healthy volunteers’ saliva samples, supra-gingival and sub-gingival bacterial plaque samples, so as to built genomic libraries. After sequencing and analyzing the results, species were annotated, and their relative abundance was calculated too. Results：The sequencing results showed that there were 15 microbial genuses in saliva samples of healthy volunteers, and there were 20 microbial genuses in samples from healthy volunteers’ supra-gingival and sub-gingival plaques. The mean relative abundance ratio of each healthy volunteers’ microorganism sample group (saliva sample group, supra-gingival sample group and sub-gingival sample group )was significantly different (P＜0.05). Conclusions：The meta-genomic method using the second generation high-throughput sequencing technique can obtain the microbial community in the oral samples of healthy volunteers well, and it is capable of helping analyze the microbial community structure in each sample group.