A total of 991 isolates of Actinomyces naeslundii were obtained from sound approximal tooth sites in either caries-active (n = 35) or caries-free (n = 20) preschool children. From this group of isolates, 101 strains were chosen to study the genotypic diversity of A. naeslundii genospecies 1 (n = 30), catalase-positive (n = 30), and catalase-negative genospecies 2 (n = 41). Polymerase chain reaction-restriction fragment length polymorphism PCR-RPLP), with a pair of primers targeting the 16S ribosome RNA gene (16S rDNA), and Mn/I digestion together with randomly amplified polymorphic DNA (RAPD) with eight arbitrary, single 10-mer primers were performed to generate genetic profiles of selected Actinomyces isolates. The hierarchic relationships of genetic profiles were finally analyzed using computerized dendrograms. There was no significant difference in the prevalence rates and proportions of either genospecies 1 or 2 between the caries-free and caries-active groups, although a higher prevalence of genospecies 2 was noted in the total population. Dendrogram analyses of the 16S rDNA PCR-RFLP profiles revealed that all strains belonging to A. naeslundii genospecies 1 could be subgrouped into three genotypes (T7, T18, and T19), with a single predominant genotype, T18 (27/30). Catalase-positive strains for genospecies 2 fell into three subtypes (T4, T7, and T17), whereas the catalase-negative counterparts were distributed amongst 16 subtypes. No specific genotype was significantly associated with caries activity. We conclude that heterogeneous subgroups of A. naeslundii genospecies 1 and 2, particularly the latter, are the constituent flora of dental plaque in children and may contribute to the pathogenesis of childhood caries.