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The aim of this paper is to investigate control strategies for functional electrical simulation (FES) cycling, with particular focus on the generation of stimulation intensities for multiple muscles, without any predetermined stimulation pattern. The control system is developed by imitating the biological neuronal control system. Specifically, the control signal on the level of joint torque (quasi-joint torque) is generated from the feedback information of lower extremities. The quasi-joint torque is then distributed to each muscle and the muscle delay is compensated, and finally, the stimulation intensity is determined. Parameters of the control system are optimized by the genetic algorithm with cost function of energy consumption and cadence error. The proposed control system is evaluated by computer simulation. The controller generates efficient stimulation even during the muscle fatigue process and successfully continues cycling without any predetermined stimulation pattern. Moreover, the controller is robust to the parameter error in the muscle delay compensator and also to the disturbances. It is expected that the proposed method would improve the FES cycling performance and relieve patients by eliminating the experimental determination of the stimulation patterns.