Aims: Comparison of the microbial composition and process performance between laboratory scale processes treating domestic and vegetable oil wastewaters. Methods and results: Two laboratory scale modified Ludzack-Ettinger processes were operated under similar operating conditions. One process was fed domestic wastewater and the other an industrial wastewater, vegetable oil effluent. Nitrogen removal capacities of the processes were similar. The industrial process exhibited a lower COD removal capacity and oxygen utilization rate, although a greater mixed liquor volatile suspended solids concentration was observed in the industrial process. Fluorescent in situ hybridization (FISH) with probes EUBmix, ALF1b, BET42a, GAM42a and HGC69a revealed that 81% and 72% of total cells stained with 4', 6-diamidino-2-phenylindole (DAPI) within the domestic and industrial processes respectively bound to EUBmix. This indicated a slightly lower Eubacterial population within the industrial process. The alpha-proteobacteria was the dominant community in the industrial process (31% of EUBmix), while the beta-proteobacteria dominated the domestic process (33% of EUBmix). Conclusions: The findings served to establish a difference in the microbial population between the processes. Therefore, the class alpha-proteobacteria could play a primary role in the degradation of vegetable oil effluent. Significance and Impact of the Study: This research will aid in process design and retrofitting of biological processes treating vegetable oil effluent.