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Single cell analysis has attracted much attention to reveal the detailed and localized biological information. Local environmental control technique is desired to analyze the detailed and localized properties of single cells. In this paper, we propose the local environmental control system with nano/micro dual pipettes to control the local reagent concentration dynamically and arbitrarily. Local environmental control by dual pipettes is applied to the rotational speed control of bacterial flagellar motor, which is a rotary molecular machine. We demonstrate quick response and iterative rotational speed control of Na+-driven flagellar motor in both accelerating and relaxing directions by switching the local spout between Na+-containing and Na+-free solutions with dual pipettes. It is shown that the rotational speed might be controllable by changing the spouting velocity of Na+-containing solution with multiplying the applied dc voltage.