An experimental validation of fractional-order PID (FOPID) controllers, which were applied to a two coupled tanks system, is presented in this article. Two FOPID controllers, a continuous FOPID (cFOPID) and a discrete FOPID (dFOPID), were implemented in real-time. The gains tuning process was accomplished by applying genetic algorithms while considering the cost function with respect to the tracking error and control effort. The gains optimization process was performed directly to the two-tanks non-linear model. The real-time implementation used a National Instruments PCIe-6321 card as a data acquisition system; for the interface, we used a Simulink Matlab and Simulink Desktop Real-Time Toolbox. The performance of the fractional controllers was compared with the performance of classical PID controllers.