In Japan, bathwaters are a potential source of legionellosis; therefore, the bathwater in public facilities must be regularly tested for Legionella spp. Currently, Legionella spp. is detected using the culture method, which is time-consuming and has limited accuracy. Moreover, the reproductive environment of Legionella spp. in bathwater remains unclear. Here, we investigated the environment in which Legionella spp. reproduce by analyzing the bathwater microbiota and its relationship with Legionella spp. We identified the microbiota of 112 bathwater samples collected from bathing facilities by sequencing 16S and 18S rRNA genes. Differences in the microbiota were observed between samples that tested positive and negative for Legionella spp., according to 16S rRNA sequencing and culture methods. Methyloversatilis, Cupriavidus, Phenylobacterium, Vermamoeba, and Aspidisca were highly correlated with Legionella spp. Our results support the development of strategies against legionellosis and elucidate the relationships between Legionella spp. and the coexisting microbiota in various environments.