We propose a sensor fusion technique for motion capture system. In our system, two kinds of sensors are used for mutual assistance. Six magnetic sensors are attached on the arms and feet for assisting twelve optical markers and six optical markers, which are attached on the arms and feet of a performer, respectively. The optical marker information is not always complete because the optical markers can be hidden due to obstacles. In this case, magnetic sensor information is used to link discontinuous optical marker information. We use a system identification technique for modeling the relation between the two signals of sensor and marker. We determine the best model from the set of candidate models using the canonical system identification technique. In order to show the efficiency of the proposed system, experiments are performed for motion capture data obtained from both the optical and magnetic motion capture system, and the animation results are shown.