This paper presents a low cost DC and AC active power filters to enhance the power quality of hybrid hydrogen Fuel Cells (FC) and Photovoltaic arrays (PV) renewable energy system through reducing the complexity of design and control of active harmonic filters that effectively mitigate power system harmonics. Its main goal was therefore to design, model and test through computer simulation, active power filters that successfully interface FC and PV to form hybrid PV/FC renewable energy system that enhance the system output power quality through the stabilization of load bus voltage and reduction of harmonic currents. Two active power filters schemes were proposed in this paper. The first system consists of a unique two stage DC Power Filter (DCPF) to regulate the DC bus voltage to its set point. The second interface scheme is the active AC Power Filter (ACPF) which served to reduce harmonic three-phase currents on the AC bus. The AC filter used on the AC bus utilizes a hysteresis current controller to generate the switching. Computer models of these two interface schemes were built and simulation studies were carried out using the Matlab/Simulink. The simulation results demonstrate the success of both power filters at meeting their primary objectives through the increased voltage stability and reduction of the Total Harmonic Distortion (THD) of current that was observed as a result of their introduction into the power system.