This investigation develops a multi-target tracking system for the motile protozoa, paramecium. The system can recognize, track and record the orbit of swimming paramecia within a 4 mm diameter of a circular experimental pool. The proposed system is implemented using an optical microscope, a CCD camera and a software tool, Laboratory Virtual Instrumentation Engineering Workbench (LabVIEW). An algorithm for processing the images and analyzing the traces of the paramecia is developed in LabVIEW. It focuses on extracting meaningful data in an experiment and recording them to elucidate the behavior of paramecia. The algorithm can also continue to track paramecia even if they are transposed or collide with each other. The experiment demonstrates that this multi-target tracking design can really track more than five paramecia and simultaneously yield meaningful data from the moving paramecia at a maximum speed of 1.7 mm/s.