The possibility to conceive a nanorobot propelled by flagellated magnetotactic bacteria is becoming a reality. But the
development of such complex systems requires the implementation of various functionalities, one of which being the
tracking of such devices with sufficient speed and accuracy. In this paper, we present an automated tracking system developed with modern computational and microscopy equipment designed to follow a bacterium through various swimming paths. The results obtained with such system are presented in order to asses the platform real-time performance in tracking MC-1 magnetotactic bacteria. This system is also used to record data related to the movement of the bacteria which may prove to be useful in other field of research besides nanorobotics.