The medical importance of free living amebas has been increasing as a worldwide problem. In Japan amebic keratitis caused by Acanthamoeba has caught the attention of ophthalmologists due to increasing risk of infection for soft-contact lens users. In the present work we examined the process of Acanthamoeba contamination in water placed indoors and outdoors under different conditions in Nagasaki city, Japan. The most frequently contaminated water was in coverless outdoor containers in the spring, and the next was in similar conditions, but in the autumn. The highest contamination of indoor water in coverless containers was found in the summer although the frequency was much lower than outdoors. When the containers were covered, complete protection for water bodies from Acanthamoeba contamination was obtained indoors, and nearly complete outdoors. Electrophoretic patterns of mitocondrial DNA fragments digested by two restriction enzymes indicated that Acanthamoeba contaminants seemed to be season-specific although the number of examined isolates was very small.