In recent years, because of the worldwide increase in antibiotic resistant bacteria, studies have been conducted on antimicrobial therapies using photodynamic therapy, which was already being used in cancer treatment29. Among the wide variety of bacteria in the oral cavity flora, the bacteria of periodontal disease are used for the study and application of aPDT in clinical practice. However, the current photodynamic therapy method is complicated, as it includes staining with a photosensitizer, and the bacterial sterilization mechanism has not been clarified18, 23, 24. In this study, we examined the sterilization mechanism of aPDT in bacterial cells using PpIX, a pigment used for energy production by P. gingivalis.