The aim of the study was to identify the number and distribution of genotypes of Streptococcus mutans (S. mutans) and Streptococcus sobrinus (S. sobrinus) isolated from caries-free and caries-active subjects. Non-stimulated saliva, buccal smooth surface of the right upper teeth, fissures of sound occlusal surface, and carious surface were sampled from 7 caries-free and 7 caries-active (DMFT ≥ 6) students aged 22-24 years. S. mutans and S. sobrinus were isolated using Chelex-100 and primarily identified by colony morphology and biochemical characteristics. The isolates of S. mutans were genotyped using arbitrarily primed polymerase chain reaction. A total of 516 isolates of S. mutans were genotyped from 47 sites in 14 students, and 44 different genotypes were determined. All of the caries-free individuals harbored S. mutans but not S. sobrinus, although individuals 3 and 7 had no S. mutans in their saliva. The CFU value of S. mutans on carious surfaces was the highest, and values in saliva, fissures, and occlusal surfaces were higher in caries-active individuals than in caries-free individuals. We detected 28 genotypes of S. mutans in caries-free individuals, each of who carried more than 3 genotypes. However, we found only 16 genotypes of S. mutans in caries-active individuals, each of who carried no more than 3 genotypes. More genotypes are harbored in the saliva, fissures, and smooth surfaces of caries-free individuals than of caries-active individuals. The proportion of samples positive for S. mutans and S. sobrinus was significantly higher in caries-active individuals than in caries-free individuals, and the presence of these species is a risk factor for high DMFT in dental caries. Isolates of S. mutans exist that have apparent genetic diversity. The genotypes of isolates might relate to differences in caries susceptibility.