SummaryObligate intracellular bacteria are commonly found as endosymbionts of acanthamoebae, however, their survival in and ability to transfer to amoebae are currently uncharacterized.In this study, six bacterial endosymbionts, found in five environmental Acanthamoeba isolates (S13, R18, S23, S31, S40) from different locations of Sapporo city, Japan, were characterized. Phylogenetic analysis revealed that three-bacterial endosymbionts (eS31, eS40a, eS23) belonged to α-and β-Proteobacterium phyla and the remaining endosymbionts (eR18, eS13, eS40b) belonged to the Chlamydiales phylum. The Acanthamoeba isolate (S40) contained two phylogenetically different bacterial endosymbionts (eS40a, eS40b). Fluorescent in situ hybridization analysis showed that all bacterial endosymbionts were diffusely localized within amoebae. Transmission electron microscopy also showed that the endosymbionts were rod-shaped (eS31, eS40a, eS23) or sphere-or crescent-shaped (eR18, eS13, eS40b). No successful culture of these bacteria was achieved using conventional culture methods, but the viability of endosymbionts was confirmed by live/dead staining and RT-PCR methods. However, endosymbionts (except eR18) derived from original host cells lost the ability to be transferred to another amoeba strain (Acanthamoebae ATCC C3). Taken together, our data demonstrate that phylogenetically diverse bacterial endosymbionts found in amoebae are viable and maintain a stable interaction with amoebae.