To measure genetic variation within and among populations of the bloom-forming cyanobacteriumMicrocystis aeruginosa, we surveyed a suite of lakes in the southern peninsula of Michigan that vary in productivity (total phosphorus concentrations of ∼10 to 100 μg liter⁻¹). Survival ofM. aeruginosaisolates 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,r²= 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 ofM. aeruginosaisolates collected from an oligotrophic lake (total phosphorus of ∼10 μg liter⁻¹and dissolved inorganic nitrogen:total phosphorus ratio of 12.75) differed among five different medium types (Gtest,Pof <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 ofM. aeruginosawere genetically diverse within and among lakes (by analysis of molecular variance, Φ_sc= 0.412 [Φ_scis 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 uniqueM. aeruginosaclones 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.