Batch experiments were conducted on the degradation of synthetic and municipal wastewater by six different strains, i.e., Agrobacterium sp., Bacillus sp., Enterobacter cloacae, Gordonia, Pseudomonas stutzeri, Pseudomonas putida. By applying a fractional factorial design (FFD) of experiments, the influence of each strain and their interactions were quantified. An empirical model predicting the treatment efficiency was built based on the results of the FFD experiments with an R(2) value of 99.39%. For single strain, Enterobacter cloacae, Gordonia and P. putida (p=0.008, 0.009 and 0.023, respectively) showed significant enhancement on organic removal in the synthetic wastewater. Positive interaction from Enterobacter cloacae, Gordonia (p=0.046) was found, indicating that syntrophic interaction existed, and their coexistence can improve total organic carbon (TOC) degradation. Verification experiments were performed to evaluate the effect of bioaugmentation by introducing three selected strains into an activated sludge reactor for treating municipal wastewater. The removal efficiency of TOC with the bioaugmentation was increased from 67-72% to 80-84% at an influent TOC concentration of 200mg/L. The results derived from this study indicate that the FFD is a useful screening tool for optimizing the microbial community to enhance treatment efficiency.