Objective To analyze the differences between the bacterial diversities in the saliva of caries-free and cariessusceptible adolescents through polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). Methods Twenty adolescent subjects aged 12-18 years were recruited and subdivided into two groups: caries-free adolescents (n=10) and caries-susceptible adolescents (n=10). Saliva samples were collected. Total DNA was isolated directly from each sample. A portion of the 16S rRNA gene locus was PCR-amplified by using universal primers. Microbial diversity was analyzed through PCR-DGGE. Results Analyzing the DGGE profile, we found that the composition of the saliva microbiome exhibited great intra-individual differences; the average band numbers of the caries-free adolescent group and the caries-susceptible adolescent group were 32.5±3.7 and 27.3±3.4, respectively. The differences between the groups were statistically significant (P=0.008). Shannon-Wiener’s indexes of the caries-susceptible adolescent group and the caries-free adolescent group were 2.5±0.2 and 2.6±0.2, respectively, but the differences between the groups were not significant (P=0.405). Clustering analysis results suggested that most of the samples in the same group clustered together; this observation showed a high community structure similarity. Conclusion The microbial diversity and complexity of bacteria in saliva are significantly higher in caries-free adolescents than in caries-susceptible adolescents. During caries development, bacterial diversity in the saliva likely decreases.