Abstract: Objevtive: To discuss the microbial differences in dental plaque of deciduous teeth between caries-active children and caries-free children. Methods: Three caries-active children and three caries-free children were selected according to WHO standard. Three specimens of plaque (from labial-buccal surfaces, lingual surfaces and caries lesions) were taken from each caries-active children and two specimens of plaque (from labial-buccal surfaces and lingual surfaces) were taken from each caries-free children. DNA of the whole genome was extracted. PCR amplification of the V1-V2 region of 16SrDNA was conducted and the gene library was constructed. The method of 454 pyrosequencing was used. The resultant sequences were classified by RDP classifier and the statistic analysis was conducted. Results: A total of 324,262 gene sequences were obtained from 15 specimens, there were 21617 gene sequences for each specimen averagely and the average length was 268 bps. In caries-active children, 5 bacterial strains were found significantly different among the different locations (P<0.05). They were Streptococcus, Propionibacterium, Corynebacterium, Leptotrichia and Lactobacillus. There were 5 bacterial strains significantly different between caries-active children and caries-free children (P<0.05), including Streptococcus, Filifactor, Solobacterium, Thermus and Brevibacillus. Conclusion: The microorganism detection rate in dental plaque is different between caries-active and caries-free children.