The objective of this study was to assess the ability of laboratory-reared and natural communities of zooplankton to graze on toxic and non-toxic strains of Microcystis during bloom events in the Transquaking River, a tributary of Chesapeake Bay. The dynamics of toxic and non-toxic strains were documented via quantification of the microcystin synthetase gene (mcyD) and ribosomal RNA gene, 16S. During the 2-year field study, Microcystis blooms were comprised of >106 cell equivalents L-1 and the percentage of toxic strains ranged from 1 to 100%. The natural microzooplankton community was able to graze on both strains of Microcystis in two-thirds of experiments, with a slight preference for the non-toxic strains in most experiments. Cultured mesozooplankters (Daphnia pulex and Hyalella azteca) grazed at least one strain (toxic or non-toxic) of Microcystis in only one-third of experiments conducted. In contrast, the wild mesozooplankton community grazed at least one strain of Microcystis in every experiment with electivity indices showing a preference towards toxic strains in most experiments. This finding demonstrates that natural mesozooplankton were better grazers of both toxic and non-toxic strains of Microcystis than their cultured counterparts. Overall, both microzooplankton and mesozooplankton were capable of grazing toxic and non-toxic strains of Microcystis with similar success and at similar rates. As such, the ability to synthesize microcystin does not seem to offer toxic Microcystis populations a significant defense against grazing by co-occurring zooplankton communities.