Biomanipulation measures in lakes, taken to diminish algal blooms, have mainly been restricted to the reduction of zooplanktivorous fish with the aim to stimulate the grazing pressure by native filter feeders such as Daphnia. However, larger filter feeders like the exotic zebra mussel, Dreissena polymorpha, have been suggested as an optional tool because of their high filtering capacity. We compared grazing by two filter feeders, D. polymorpha and Daphnia galeata, offered seston from Lake IJsselmeer, the Netherlands in two consecutive years: 2002 and 2003. The seston in both years was dominated by the colony-forming cyanobacterium Microcystis aeruginosa. The grazing studies were performed under controlled conditions in the laboratory and samples were analyzed on a flow cytometer, making it possible to quantify grazing on different seston components and size fractions, including cyanobacteria, other phytoplankton (green algae, diatoms, etc.), and detritus. No differences in clearance rates, on a per weight basis, were found between the two grazer species. The clearance rate on cyanobacteria (especially <20 microm) was lower in 2003 than in 2002. In 2003, the microcystin concentration of cyanobacteria was higher than in 2002, suggesting that the observed lower clearance rate in 2003 was due to the enhanced toxin content of the cyanobacteria. Zebra mussels, although indiscriminately filtering all seston groups out of the water, positively selected for phytoplankton in their mantle cavity, irrespective of its toxicity, and rejected detritus. Since no differences in clearance rates were found between the two grazer species, we conclude that for biomanipulation purposes of shallow lakes, native species like the daphnids should be preferred over exotic species like zebra mussels. When the seston is dominated by phytoplankton that cannot be filtered out of the water column by Daphnia, however, the use of zebra mussels may be considered. Care should be taken, however, in the choice of the lakes since the mussels may have severe ecological and economic impacts.