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As a new approach of power sources and novel sensing and driving devices, the living microorganism has become a part of miniature robot. The basic work of this research is continuous observation of a single swimming microorganism without fixed in a sufficiently large working area. We developed a novel system for tracking motile microorganism and evaluating its motility. The system can track a freely swimming microorganism two dimensionally by moving a XY stage based on visual feedback control to keep the target cell in the center area of the field of optical microscope view. Also, the vision system can record the morphological and motive parameters of the target cell and process images using two imaging modes including bright filed and phase contrast at the magnification of 40 times. Experimental results demonstrated the real-time tracking of a Chlamydomonas reinhardtii cell moving at a average velocity of 150 mum/s for 300 seconds with the 40x objective.