This paper proposes a fractional-order sliding mode controller (FOSMC) for the robust control of a nonlinear process subjected to unknown parametric disturbances. The controller aims to ensure optimal growth in photobioreactors of native microalgae involved in eutrophication of the Sinaloa rivers in Mexico. The controller design is based on the Caputo fractional integral-order derivative and on the convergence properties of a sliding surface. For nonlinear systems, the proposed FOSMC guarantees convergence to the sliding surface even in the presence of model disturbances. The proposed controller is compared to an Internal Model Control (IMC) through numerical simulations.