In recent years, excessive anthropogenic nutrient loading in Taihu (Lake Tai), China's third largest freshwater lake, has promoted the growth of harmful cyanobacterial blooms. Often composed of toxic species, these blooms threaten the supply of drinking water and fisheries-related food supplies for more than 8 million people. During a spatial survey in May 2009, surface water samples were collected from 14 stations located throughout this 2338km2 lake. Physicochemical and toxin measurements were compared to results from PCR based analyses of extracted DNA to examine microbial community diversity. Maximum concentrations of the hepatotoxin microcystin in this region were >600μgg−1 dry weight. Statistical comparisons of lake chemistry demonstrate relationships between toxin concentrations and physicochemistry (e.g., temperature, nutrients) within the water column. Pyrosequencing of bacterial 16S rRNA gene fragments revealed a diverse community that includes potential fecal bacteria. However, subsequent source tracking of specific fecal bacteria (by quantitative PCR) indicated that fecal bacteria concentrations in the lake water bacteria were relatively low and likely not of human origin. In total the data suggest that the proliferation of cyanobacteria, but not the production of microcystin, is influenced (and perhaps regulated) by both nitrogen and phosphorus concentrations. Our observations further suggest that microcystin concentrations are correlated to the diversity of the eubacterial community, implying that specific bacteria may associate with bloom events and/or be associated with nutrient sources loading into this system.