The aim of this study was to clarify the genotypic stability of mutans streptococci (MS) longitudinally during orthodontic treatment. Plaque samples were obtained from the supragingival smooth surface of the upper right teeth at four stages: prior to and after 1, 3 and 6 months of orthodontic treatment. Levels of total viable count, total streptococci and MS in dental plaque of 17 patients were recorded. Streptococci isolated from dental plaque samples were identified as MS on the basis of their morphological and biochemical properties. DNA was prepared from 713 strains of MS and the strains were then identified with polymerase chain reaction (PCR) again. Arbitrarily primed PCR (AP-PCR) fingerprinting was applied in determining the genotypes of MS. The results indicated that levels of total viable count, total streptococci and MS increased significantly after the fixed appliances were bonded. A maximum of 3 different genotypes were found in an individual. All the genotypes were found again after the application of the fixed appliances in 17 patients. A new AP-PCR typing pattern was found after the application of fixed appliances for 1 month in patient 1. That strain was not detected either prior to or after 3, or 6 months of treatment. The result indicated that the MS clones were very stable during orthodontic treatment.