The analysis of functional groups with a resolution to the individual species level is a basic requirement to better understand complex interactions in aquatic food webs. Species-specific stable isotope analyses are currently applied to analyse the trophic role of large zooplankton or fish species, but technical constraints complicate their application to smaller-sized plankton. We investigated rotifer food assimilation during a short-term microzooplankton bloom in the East African soda lake Nakuru by developing a method for species-specific sampling of rotifers. The two dominant rotifers, Brachionus plicatilis and Brachionus dimidiatus, were separated to single-species samples (purity >95%) and significantly differed in their isotopic values (4.1 parts per thousand in delta C-13 and 1.5 parts per thousand in delta N-15). Bayesian mixing models indicated that isotopic differences were caused by different assimilation of filamentous cyanobacteria and particles A main difference was that the filamentous cyanobacterium Arthrospira fusiformis, which frequently forms blooms in African soda lakes, was an important food source for the larger-sized B.plicatilis (48%), whereas it was hardly ingested by B.dimidiatus. Overall, A.fusiformis was, relative to its biomass, assimilated to small extents, demonstrating a high grazing resistance of this species. In combination with high population densities, these results demonstrate a strong potential of rotifer blooms to shape phytoplankton communities and are the first in situ demonstration of a quantitatively important direct trophic link between rotifers and filamentous cyanobacteria.