The position control of flexible joint manipulator is investigated by applying the self-organizing fuzzy logic controller (SOC) proposed by Procyk and Mamdani. The SOC is a heuristic rule-based controller and a further extension of an ordinary fuzzy controller, which has a hierachy structrue which consists of an algorithm being identical to a fuzzy controller at the lower ollp and a learning algorithm accomodating the performance evalution and rule modification function at the upper ollp. This form of control can be used in those complex systems which have been too difficult to control or which in the past have had to rely on the experience of a human operator. Even though the significant dynamic coupling of the motors and links on the flexible joint manipulator, the performance of command-following is good by applying the proposed SOC.