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In a laser tracking system (LTS) the control objective is for a laser beam to track a retro-reflecting moving target through adjustment of joint angles and velocities of a two-degrees-of-freedom (DOF) tracking gimbal on which tracking mirrors are mounted. This is done based on two types of feedback signals: distance reading, obtained by a laser interferometer and off-center distance error of the returning laser beam, as measured by a four-quadrant photodetector. The LTS control system should effectively overcome noise disturbances originating from the system itself as well as the environment, and coupling effects existing in the tracking system. A complete LTS consists of laser interferometer transducer subsystem, opto-electronic beam steering subsystem, gimbals driving subsystem and the digital control subsystem. As high-tracking accuracy and high-tracking speed are both vital for LTS operation, a design of a high-performance controller is critical. This brief shows that fuzzy logic controllers (FLC) can outperform classic proportional-integral-derivative (PID) controllers in such applications. Disturbances and nonlinearities existing in the LTS developed at the Florida Atlantic University (FAU) Robotics Center are discussed and analyzed, and an experimental-based design and implementation of a mixed-mode FLC to suppress such coupling effects and nonlinearities, which cannot be handled by PID controllers, are studied. The advantages of utilizing a phase-shifted FLC to improve the control performance for a system with a relatively long time delays is confirmed by simulation and experimental results. A comparison between the performances of PID and FLC is presented.