Balamuthia mandrillaris is an environmentally derived, free-living amoeba that causes fatal meningoencephalitis. We previously isolated B. mandrillaris from soil in the Aomori Prefecture and attempted to culture the cell-free amoeba using liquid medium; however, this was difficult to achieve because of contamination of the medium with endogenous bacteria. The aim of this study was to determine the presence of endogenous bacteria in environmentally derived B. mandrillaris and identify bacteria. Two new environmentally derived B. mandrillaris strains were isolated from soil samples collected throughout Japan. Environmentally derived B. mandrillaris was cultured under nutrient-free conditions for 60 days, and the induced cysts contained large amounts of viable bacteria. The sequence of the endophytic bacteria revealed that the genus Chitinophaga was common between the two strains of B. mandrillaris. The opportunistic pathogens Inquilinus and Brevundimonas were also detected. All of these bacteria were pigment-producing species. Bacterial pigment production helps protect organisms from extremes of heat and cold, increases the virulence of pathogenic strains, and protects organisms from protein and DNA damage caused by UV light and ionizing radiation. This suggests that B. mandrillaris preserving bacteria in a viable state for a long time under severe conditions with no nutrition may be the ability of the bacteria to produce pigments.