A recycling reactor system operated under sequential anoxic and oxic conditions for the treatment of swine wastewater has been developed, in which piggery slurry is fermentatively and aerobically treated and then part of the effluent is recycled to the pigsty. This system significantly removes offensive smells (at both the pigsty and the treatment plant), BOD and others, and may be cost effective for small-scale farms. The most dominant heterotrophic were, in order, Alcaligenes faecalis, Brevundimonas diminuta and Streptococcus sp., while lactic acid bacteria were dominantly observed in the anoxic tank. We propose a novel monitoring system for a recycling piggery slurry treatment system through the use of neural networks. In this study, we tried to model the treatment process for each tank in the system (influent, fermentation, aeration, first sedimentation and fourth sedimentation tanks) based upon the population densities of the heterotrophic and lactic acid bacteria. Principal component analysis(PCA) was first applied to identify a relationship between input and output. The input would be microbial densities and the treatment parameters, such as population densities of heterotrophic and lactic acid bacteria, suspended solids(SS), COD, NH$_4$(sup)+-N, ortho-phosphorus (o-P), and total-phosphorus (T-P). then multi-layer neural networks were employed to model the treatment process for each tank. PCA filtration of the input data as microbial densities was found to facilitate the modeling procedure for the system monitoring even with a relatively lower number of imput. Neural network independently trained for each treatment tank and their subsequent combined data analysis allowed a successful prediction of the treatment system for at least two days.