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We developed a novel separation system to isolate target microorganisms from a large heterogeneous population by a local viscosity control. A sol-gel transformation material is mixed with the sample solution and we controlled the state from sol to gel and gel to sol reversibly based on the temperature change by heating of the microelectrode and laser irradiation near the target. The sample solution is pumped in the microchannel near the bottom surface with the vertical sheath flow. The selected microorganisms are fixed on the bottom surface of the microchannel by the pinpoint gelation. The other objects suspended in the microchannel are removed by the cleaning flow in the microchannel. Process of retaining, cleaning and isolation of the target microbe was realized easily. Based on this method, we propose a microreactor on a chip for several biological experiments with the selected microbes.