Abstract: Objective To evaluate the difference in microbial diversity between ECC children before treatment and after treatment by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Methods 22 children aged 3-5 years old from Peking University Yandong Kindergarten were selected for this study. Saliva samples were collected before treatment and 2 weeks after treatment. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. Then the PCR products were isolated using DGGE method. Results The mean species richness of the bacterial population was greater in the samples collected after treatment (28±4.1) than in those before treatment (23±2.9). The difference was statistically significant (P<0.01). Phylogenetic analysis show similarity within the groups while difference between groups. Conclusions PCR-DGGE method can visualize the diversity and complexity of the microbial biota associated with caries and monitor the dynamic changes of the bacterial compositions.