Sequencing batch reactors (SBR) are often used for research on nutrient removal systems. A model anaerobic-oxic SBR was compared with a compartmentalized continuous-flow system. The levels of COD, phosphorus, and nitrogen removal in both systems were comparable but the biocenoses differed significantly. The SVI values of activated sludge from the continuous reactor ranged between 100 and 200 ml/g although no significant occurrence of filamentous microorganisms was observed. The sequencing batch reactor produced activated sludge with the SVIs below 100 ml/g and with high settling velocities. Filamentous microorganisms were frequently observed in the biocenosis of the SBR. The differences in settling properties and filamentous growth in both reactors are discussed and explained.