BACKGROUND Early childhood caries (ECC), despite being a preventable disease, remains prevalent in sub-Saharan Africa. This study compared the occurrence of Streptococcus mutans and Streptococcus sobrinus in dental plaque from caries free and caries active Nigerian preschool children. METHODS Structured questionnaire were administered to eighty (80) mothers to inquire about the sociodemographic characteristics of their children. Diagnosis of dental caries was made according to the diagnostic criteria of the World Health Organization (WHO). Supragingival plaque sample collected from caries free children and children with dental caries (cavitated and non-cavitated lesions) using wooden toothpicks were cultured anaerobically. Samples were cultured in anaerobiosis and isolates obtained were identified based on molecular characterization performed by polymerase chain reaction (PCR) analysis. Statistical package for the social sciences (SPSS 25.0) was used for analysis. RESULTS Streptococcus mutans was detected in 26(65.0%) children with early childhood caries, and S. sobrinus in 10(25.0%) children with early childhood caries. The presence of S. mutans and S. sobrinus occurring together was associated with a higher deft score. Occurrence of S. mutans did not show significant difference between children with ECC and caries free children (p=0.099), however, the proportion of children with ECC positive for S. sobrinus was significantly higher than that of caries free children (p= 0.003). CONCLUSIONS S. mutans and S. sobrinus had a similar frequency of occurrence in children with ECC and caries free children. The occurrence of S. mutans alongside S. sobrinus in ECC is related to its severity.