From laboratory research and a literature review of the biochemical pathways of aerobic-facultative heterotrophic organisms, an hypothesis is proposed for the proliferation of anoxic-aerobic (AA) filamentous organisms in nitrification-denitrification (ND) and nitrification-denitrification biological excess phosphorus removal (NDBEPR) systems. In activated sludge, under anoxic conditions floc-forming organisms execute the denitrification of nitrate (NO3) through each of the denitrification intermediates to dinitrogen (N2), in the process of which the intermediate nitric oxide (NO) is accumulated intracellularly. Intracellular NO is inhibitory to the utilization of oxygen in the subsequent aerobic zone. In contrast, the filamentous organisms execute only part of the denitrification pathway, i.e. the reduction of NO3 to NO2; they do not accumulate NO and hence are not inhibited in the subsequent aerobic zone. Thus in anoxic-aerobic systems, floc-formers are placed at a disadvantage in the aerobic zone giving an advantage to the filaments in the competition for substrate. Experimental evidence to support this hypothesis is presented and a tentative proposal of a strategy for control of AA filament proliferation is described and tested experimentally.