Background: The aim of this study was to assess the relationships of quantitative salivary levels of mutans streptococci (MS) in children, aged 3–6 years and 12–15 years, exhibiting variable patterns of caries activity, and to compare the association of MS in saliva using microbial and molecular (polymerase chain reaction [PCR]) assay. Materials and Methods: In this cross-sectional observational study, eighty children were included, forty children each in Group I (3–6 years) and Group II (12–15 years). Children were further divided into two subgroups (Group IC, INC and Group IIC, IINC) based on their dental caries status. Saliva samples were collected and plated onto Mitis Salivarius-Bacitracin agar plates. After detection of MS, DNA was isolated and purified, and MS were evaluated using the PCR and AP-PCR. Results: Of the selected 80 children, 42 were male and 38 were female. In Group IC, the mean colony count was 2.27 ± 0.54 × 105 CFU/ml, and in Group INC, the mean colony was found to be 1.61 ± 0.54 × 105 CFU/ml. In Group II, where mean colony count of 3.31 ± 0.85 × 105 CFU/ml and 2.44 ± 0.54 × 105 CFU/ml was observed in Group IIC and Group IINC, respectively. Conclusion: The mean colony count increased with increasing age and was also more in children with dental caries. Based on the matrices generated by the PCR analysis using coefficient slipped-strand mispairing, wide range of genetic diversity was seen in cases of children with and without clinically detectable caries.