The anaerobic–anoxic sequence batch reactor (A2SBR) was applied to achieve nitrogen and phosphorus removal in an energy-saving sewage treatment system involving an up-flow anaerobic sludge blanket combined with a down-flow hanging sponge reactor to treat municipal sewage. After sludge acclimation, the A2SBR showed satisfactory denitrification and phosphorus removal performance with total phosphate and nitrate concentrations of the effluent of 8.4 ± 3.4 mg-N L–1 and 0.9 ± 0.6 mg-P L–1, respectively. 16S rRNA gene sequence and fluorescence in situ hybridization analyses revealed that ‘Candidatus Accumulibacter phosphatis’ was the dominant phosphate-accumulating micro-organism. Although a competitive bacterium for polyphosphate-accumulating organisms, ‘Ca. Competibacter phosphatis’, was not detected, Dechloromonas spp. were abundant. The ppk1 gene sequence analysis showed that the type II lineage of ‘Ca. Accumulibacter’ was dominant. The results suggest that denitrification and phosphorus removal in the A2SBR could be achieved by cooperative activity of ‘Ca. Accumulibacter’ and nitrate-reducing bacteria.