Fluorescence in situ hybridization (FISH) was used to analyse the community composition of a sequencing batch reactor (SBR) operating with aerobic-anaerobic cycling and fed acetate as its sole carbon source. Phosphorus was removed from the SBR microbiologically. Marked shifts in the community structure occurred as the phosphorus/carbon (P/C) ratio in the feed was changed. When the P/C ratio was shifted from 1:10 to 1:50, FISH analysis showed that the percentage of beta-Proteobacteria fell from ca 77% of the total bacteria to ca 38%. This decrease in the beta-Proteobacteria coincided with a reduction in both the proportions of the beta-proteobacterial Rhodocyclus-related phosphorus-accumulating bacteria and the biomass phosphorus content. FISH/microautoradiography and FISH/poly beta-hydroxyalkanoate (PHA) staining showed that the Rhodocyclus-related bacteria assimilated acetate and synthesized PHAs anaerobically, and that they accumulated phosphorus aerobically. No Acinetobacter spp. could be detected in any of the communities, casting further doubt on their role in phosphorus-removing activated sludge systems. As the feed P/C ratio decreased there was a corresponding increase in the proportion of alpha-Proteobacteria and, to a smaller extent, in the proportion of gamma-Proteobacteria; both the alpha- and gamma-Proteobacteria consisted mostly of tetrad-forming cocci, fitting the description of the so-called 'G-bacteria' morphotype. The change in the proportions of Proteobacteria present paralleled increases in the biomass glycogen content. Both the alpha- and beta-proteobacterial 'G-bacterial' populations assimilated acetate and synthesized PHA anaerobically. The alpha-Proteobacteria are considered responsible for glycogen production in these SBR systems.