The Acanthamoeba genus is an opportunistic protozoan parasite which has adapted to live in a variety of environments, including soil, air, fresh water, ocean sediment, wild animals, and humans. Some Acanthamoeba species have been determined to induce serious human infections, including amoebic keratitis, particularly in contact lens wearers, as well as granulomatous amoebic encephalitis (GAE) in immunocompromised individuals (Marciano-Cabral and Cabral, 2003). Amebic keratitis was considered to be a relatively rare type of corneal infection during the 10 years following the first case report by Jones et al. (1975). However, the incidence of amoebic keratitis Abstract: The endosymbionts of 4 strains of Acanthamoeba (KA/E9, KA/E21, KA/E22, and KA/E23) isolated from the infected corneas of Korean patients were characterized via orcein stain, transmission electron microscopic examination, and 16S rDNA sequence analysis. Double membrane-bound, rod-shaped endosymbionts were distributed randomly throughout both the trophozoites and cysts of each of Acanthamoeba isolates. The endosymbionts of KA/E9, KA/E22, and KA/E23 were surrounded by electron-translucent areas. No lacunae-like structures were observed in the endosymbionts of KA/E21, the bacterial cell walls of which were studded with host ribosomes. Comparative analyses of the 16S rDNA sequences showed that the endosymbionts of KA/E9, KA/E22 and KA/E23 were closely related to Caedibacter caryophilus, whereas the KA/E21 endosymbiont was assigned to the CytophagaFlavobacterium-Bacteroides (CFB) phylum. In the 4 strains of Acanthamoeba, the hosts of the endosymbionts were identified as belonging to the Acanthamoeba castellanii complex, which corresponds to the T4 genotype. Acanthamoeba KA/E21 evidenced characteristics almost identical to those of KA/E6, with the exception of the existence of endosymbionts. The discovery of these endosymbionts from Acanthamoeba may prove essential to future studies focusing on interactions between the endosymbionts and the amoebic hosts.