This paper addresses the problem of optimization of hydrogen production in continuous anaerobic digesters utilizing an model predictive control (MPC) strategy. The process is described by a dynamic nonlinear model. The influent COD concentration together with the effluent substrate and product concentrations are considered as state variables and estimated by an asymptotic online observer from measurements of gas composition and gas flow rate. It is experimentally demonstrated that a 75% increase of the hydrogen production can be obtained using the influent flow rate as the main control variable while keeping the conversion of the influent COD concentration higher than 95 %.