Aim: The purpose of the present study was to evaluate the relationship between infection with cariogenic bacteria or periodontal pathogens and the oral condition of children in the primary and mixed dentition stages. Method: Children aged 3 to 11 years were selected. Detection of cariogenic and periodontopathic bacteria and single nucleotide polymorphism (SNP) analyses were performed, and the prevalence of infection with cariogenic bacteria or periodontal pathogens based on caries experience and dental stage was compared. Results: The prevalence of Streptococcus mutans in both stages was significantly higher in the caries group than in the caries-free group. The prevalence of Streptococcus sobrinus was significantly higher in the caries group only in the mixed dentition stage. The prevalence of periodontal pathogens was significantly higher in the mixed dentition stage than in the primary dentition stage, regardless of caries experience. However, there were no significant differences in the prevalence of the periodontal pathogens between the primary dentition and mixed dentition stages, based on caries experience. Conclusion: Our data suggested that cariogenic and periodontopathic bacteria have different infection patterns, and that the period of infection with these bacteria also differs.

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