ABSTRACT Legionella is an important waterborne pathogen that causes Legionnaires' disease (LD). Several outbreaks associated with wastewater treatment plants (WWTPs) have been reported in recent years; however, the prevalence of Legionella in WWTPs in Japan has rarely been investigated. In this study, we investigated the distribution of Legionella in influent wastewater collected from two WWTPs in Kobe, Japan between April 2023 and March 2024. The concentrations for Legionella in all seasons varied between 104 and 106 copies/100 mL in all seasons. Among the 10 Legionella species detected in the influent wastewater, Legionella pneumophila was the most commonly isolated. Genotyping revealed that pathogenic L. pneumophila strains were widely distributed in the influent wastewater in Japan with genetic diversity. LD is one of the most important infectious diseases during natural disasters. This study highlights the importance of influent wastewater as a potential source of LD in Japan, where natural disasters occur frequently.