Porphyromonas gingivalis is important in the development of marginal periodontitis. However, the precise role and localization of P. gingivalis in chronic periapical periodontitis remain unclear. Thus, methods that can detect P gingivalis in formalin-fixed and paraffin-embedded (FFPE) tissue samples are needed. We assessed a technique combining loop mediated isothermal amplification (LAMP) with PCR (PCR-LAMP) for detection of P gingivalis, using 110 FFPE tissue samples of chronic apical periodontitis. PCR-LAMP specifically detected P gingivalis with high sensitivity in FFPE tissue samples, and the sensitivity of the technique was higher than that of PCR or LAMP alone. The results of immunohistochemistry (IHC) confirmed the specificity of PCR-LAMP. IHC showed that P gingivalis was localized hi a granular layer of chronic apical periodontitis, a region that correlated with the localization of macrophages. This is the first study to describe the localization of P gingivalis in human periapical periodontitis. In conclusion, PCR-LAMP was an effective tool for detecting P gingivalis in periapical periodontitis. In addition, IHC results improve our understanding of the role of P gingivalis in the progression of periapical periodontitis.