In this study, a new optimized nonlinear controller is designed for heat transfer part of a polymerase chain reaction machine (Thermal Cycler). Polymerase chain reaction is an important molecular technique which is performed in a Thermal Cycler to amplify a specific region of DNA. The main part of Thermal Cycler is a Peltier, which raises and lowers the temperature of the block in discrete, pre-programmed steps in several cycles. Based on the theoretical model, the goal was achieved using genetic algorithm in extended feedback linearization control system. The new optimized control structure was verified with improved temperature-tracking performance compared to earlier designs on reduced overshoot (0.3°C) and settling time (3.5-4.5 s faster). Also, the validation of the proposed method has been performed through simulation.