In this study, the growth medium temperature in a batch bioreactor was controlled at the set point by using fuzzy model-based control method. Fuzzy control parameters which are membership functions and relation matrix were found using genetic algorithm. Heat input given from the immersed heater and the cooling water flow rate were selected as the manipulated variables in order to control the growth medium temperature in the bioreactor. Controller performance was tested in the face of different types of input variables. To eliminate the noise on the temperature measurements, first-order filter was used in the control algorithm. The achievement of the temperature control was analyzed in terms of both microorganism concentration which was reached at the end of the stationary phase and the performance criteria of Integral of the Absolute Error. It was concluded that the cooling flow rate was suitable as manipulated variable with regard to microorganism concentration. On the other hand, performance of the controller was satisfactory when the heat input given from the immersed heater was manipulated variable.