To identify mechanisms underlying the bacterial inactivation process by atmospheric nonthermal plasma using a unique plasma jet that can generate various gas plasmas, Staphylococcus aureus were irradiated with carbon dioxide plasma, which produces a large amount of singlet oxygens, and nitrogen plasma, which produces a large amount of OH radicals. And damaged areas of plasma-treated bacteria were observed by field emission scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. As a result, bacteria were damaged by both gas plasmas, but the site of damage differed according to gas species. Therefore, it suggests that singlet oxygen generated by carbon dioxide plasma or other reactive species caused by singlet oxygen contributes to the damage of internal structures of bacteria through the cell wall and membrane, and OH radicals generated by nitrogen plasma or other reactive species derived from OH radicals contribute to damage of the cell wall and membrane.