Background: We aimed at determining whether the pathogenic bacteria at the onset of disease are genetically different and whether this affects future choice of the therapeutic methods against group A β-hemolytic streptococcal acute pharyngitis/tonsillitis. Methods: A pharynx swab was collected from pediatric patients who visited our hospital. The swab was cultured, and hemolytic streptococcus was detected 230 times. We isolated pathogenic bacteria of patients infected more than once and examined the bacteria using pulse-field gel electrophoresis. Results: Based on gene search results, we found that if the period of developing relapse was within 1 month from the first infection, all patients had the same gene. However, all patients in whom reinfection occurred after 6 months or later had different pertinent genes. Conclusions: The number of relapse/reinfection is significant for this disease, and considerably caution is essential for its treatment. No changes to antibacterial drug administration may be necessary for the second administration unless more than 6 months have passed since the first infection.