This work describes the performance and microbial diversity in a sequencing batch reactor of a decentralized full-scale system for urban wastewater treatment under limited aeration. The removal efficiency was: 83% for soluble chemical oxygen demand (SCOD), 60% for N-NH4+, 70% for total suspended solids (TSS) and 80% for volatile suspended solids (VSS). The biomass concentration had a maximum value around 8.7 gVSS L-1 for organic load rate of 0.6 gCOD L-1 d(-1). The food/microorganism ratios showed average of 0.2 gCOD/gVSSd. The sludge bacterial flocs were formed an irregular arrangement with organisms attached such as Euglypha sp. and pedunculate ciliates. It was observed the presence of Bacteria domains including Nitrosomonas spp., Nitrobacter spp., Nitrospira and C. "Accumulibacter" cluster. The DPAO activity was 70%. Denaturing gradient gel electrophoresis showed changes in ribotype number over biological treatment time among the groups observed being some are linked to nutrient removal. The reactor showed viability to treat domestic wastewater. (C) 2013 Elsevier Ltd. All rights reserved.