This paper is concerned with the modeling and identification of sequencing batch reactor (SBR) via genetic algorithm based polynomial neural network (GA-based PNN). The model describes a biological SBR used in the wastewater treatment process fur nitrogen removal. A conventional polynomial neural network (PNN) is applied to construct a predictive model of SBR process fur nitrogen removal before. But the performances of PNN depend strongly on the number of input variables available to the model, the number of input variables and type (order) of the polynomials to each node. They must be fixed by the designer in advance before the architecture is constructed. So the trial and error method must go with heavy computation burden and low efficiency. To alleviate these problems, we propose GA-based PNN. The order of the polynomial, the number of input variables, and the optimum input variables are encoded as a chromosome and fitness of each chromosome is computed. Simulation results have shown that the complex SBR process can be modeled reasonably well by the present scheme with a much simpler structure compared with the conventional PNN model.