To measure genetic variation within and among populations of the bloom-forming cyanobacterium Microcystis aeruginosa, we surveyed a suite of lakes in the southern peninsula of Michigan that vary in productivity (total phosphorus concentrations of ϳ10 to 100 g liter ؊1 ). Survival of M. aeruginosa isolates from lakes was relatively low (i.e., mean of 7% and maximum of 30%) and positively related to lake total phosphorus concentration (P ؍ 0.014, r 2 ؍ 0.407, n ؍ 14). In another study (D. F. Raikow, O. Sarnelle, A. E. Wilson, and S. K. Hamilton, Limnol. Oceanogr. 49:482-487, 2004), survival rates of M. aeruginosa isolates collected from an oligotrophic lake (total phosphorus of ϳ10 g liter ؊1 and dissolved inorganic nitrogen:total phosphorus ratio of 12.75) differed among five different medium types (G test, P of <0.001), with higher survival (P ؍ 0.003) in low-nutrient media (28 to 37% survival) than in high-nutrient media. Even with the relatively low isolate survivorship that could select against detecting the full range of genetic variation, populations of M. aeruginosa were genetically diverse within and among lakes (by analysis of molecular variance, ⌽ sc ؍ 0.412 [⌽ sc is an F-statistic derivative which evaluates the correlation of haplotypic diversity within populations relative to the haplotypic diversity among all sampled populations], P ؍ 0.001), with most clones being distantly related to clones collected from lakes directly attached to Lake Michigan (a Laurentian Great Lake) and culture collection strains collected from Canada, Scotland, and South Africa. Ninety-one percent of the 53 genetically unique M. aeruginosa clones contained the microcystin toxin gene (mcyA). Genotypes with the toxin gene were found in all lakes, while four lakes harbored both genotypes possessing and genotypes lacking the toxin gene.The effects of grazers or nutrients on harmful phytoplankton blooms (HABs) or HAB toxins show high temporal and spatial variability (10,42,43,47,51). One source of this variation could be genetic dissimilarity among HAB populations. For example, toxic and nontoxic genotypes within a HAB species might dominate in different habitats and at different times, which could lead to variation in, for example, the ability of consumers to control HABs. However, few studies have measured the genetic composition of HAB populations across time (28, 29) or space (2, 25), limiting our ability to assess the degree to which environmental variation may select for genotypes with different ecological traits.In freshwater systems, HABs are largely caused by cyanobacteria of the genera Anabaena, Aphanizomenon, Cylindrospermopsis, Microcystis, and Oscillatoria. Among these taxa, Microcystis aeruginosa is one of the most ecologically damaging species due to its prevalence in bodies of water that vary in nutrient loading and its degree of toxicity to aquatic and terrestrial organisms (7,11). Further, we note recent reports showing that the ongoing invasion of freshwaters in North America by the filter-feeding ze...