In this study, algae cultivation using the photobioreactor has been applied to remove the nitrogen and phosphorus compounds in the wastewater of the livestock industry. The optimal ratio of nitrate and ortho-phosphate concentration was found for the enhancement of removal efficiency. To achieve the high density culture of algae, the photobioreactor consisted of optical fibers wes developed to get the sufficient light intensity. The light could be illuminated uniformly from light source to the entire reactor by the optical fibers. The structured kinetic model was proposed to describe the growth rate, consumption rate of nitrates and ortho-phosphates in algae culture. The self-organizing fuzzy logic controller incorporated with genetic algorithm was constructed to control the semi-continuous wastewater treatment system. The proposed fuzzy logic controller was applied to maintain the nitrated concentration at the given set-point with the control of wastewater feeding rate. The experimental results showed that the self-organizing fuzzy logic controller could keep the nitrate concentration and enhance algae growth.