We asked if intraspecific variation within a population of the toxic, bloom-forming phytoplankter, Microcystis aeruginosa, leads to differential vulnerability to grazing by the invasive, filter-feeding zebra mussel (Dreissena polymorpha). We performed two series of laboratory feeding experiments in which D. polymorpha were presented with several different sympatric M. aeruginosa clones in a two-species mixture with the high-quality, nutritious alga, Ankistrodesmus falcatus. Mean selectivity across M. aeruginosa clones ranged from near zero (i.e., no feeding on M. aeruginosa) to near one (equal feeding on the two algal species), evidence of maximal variation in grazing vulnerability across twenty clones of M. aeruginosa—a species assumed to be largely ‘inedible’ to grazers—from the same population. This range of vulnerability is essentially equal to that typically measured across all phytoplankton species. Large intraspecific variation in grazing vulnerability, and its ecological consequences, could influence the promotion or control of noxious blooms of toxigenic cyanobacteria.