In this work a GA-based optimization is used to find the optimal scaling parameters of a fuzzy logic-based MPPT controller, that maximize the efficiency of a photovoltaic pumping system. The tuning of input and output parameters are of direct effect on the power that flows from the photovoltaic source to the load. In order to see concrete results, the PV system is used for irrigation of greenhouses in Laghouat, Algeria. The performances of the proposed GA-based fuzzy controller are compared with those obtained using a fuzzy logic-based MPPT controller without optimization under high and quick variations of meteorological conditions. The simulation results proved a good robustness performance of the proposed controller over the other one regarding the gained solar energy and the daily pumped water.