This paper deals with the optimization of a parallel hybrid Fuel Cell (FC)/ Ultracapacitors (UCs) power source for automotive applications. The aim of this hybridization and its control are to fulfil the load requirements as well as to comply with the component constraints (high efficiency, reduced weight and cost, etc.). First, a classical hybrid architecture using FC/UCs and a two-converter structure is presented. After that, power requirements for automotive applications are analyzed, and the load power demands for the FC/UCs sources are deduced. Secondly, the model-based design approach is used for the optimization, and a selection of the main components to be optimized is presented. Thus, the simulation model and the control strategy are detailed. This model has been validated experimentally. Finally, an optimization algorithm is designed using Parallel Computing and the Genetic Algorithm toolbox of Matlab/Simulink. The retained criterion is based on the reduction of the total volume of the system.