BACKGROUND: Due to the complexity of nonlinear and biochemical phenomena involved in anaerobic wastewater treatment units, efficient operation and control is limited and difficult. The objective of this study was to implement a new multi-objective control strategy to simultaneously optimise the effluent chemical oxygen demand (COD eff ) and the biogas flow rate (Q gas ) in an anaerobic bioreactor using non-dominated sorting genetic algorithms-II (NSGA-II) and genetic algorithm-artificial neural network (GA-ANN). The novel approach considered two operational objectives, i.e. control of the effluent quality and control of the maximum production rate of biogas, and took advantage of the difference between the dynamics of the liquid and gas phases using variables from both phases.