For the purpose of evaluating the appropriateness of AP-PCR as a facile, rapid and reproducible method for genotyping Streptococcus mutans, and selecting the discriminant primer for it, a DNA fingerprinting was performed on the microorganisms isolated from caries-free children and children with rampant caries, respectively. In the course of selecting appropriate primer for S. mutans genotyping, we chose S2 primer from 6 different primers which shows highest resolution on the agarose gel as well. Nineteen kinds of fingerprint patterns were observed in caries-free children and children with rampant caries which were produced by combination of 7 different fragments. Interestingly, the number of types observed in caries-free children was greater than that in children with rampant caries. And we observed Type 2 was predominant in children with rampant caries (about 80%) and relatively even distribution of each types in caries-free children. Furthermore, it was appeared that the major types in normal control were not or rarely found in children with rampant caries. In conclusion, we could establish simple, rapid and highly reproducible AP-PCR method for genotyping S. mutans. We also found differences in distribution of S. mutans between normal and patient, which suggested that cariogenicity is also dependent on qualitative aspects which is caused by the difference in genotypes of S. mutans in oral cavity.