In August of 2003 and August of 2004, blooms of potentially toxic cyanobacteria Microcystis spp. persisted in western Lake Erie. Samples collected from the bloom were analyzed for the cyanobacterial toxin microcystin and the presence of Microcystis spp. cells. Estimates of microcystin toxicity exceeding 1 microg L(-1) (microcystin-LR activity equivalents), the safety limit set by the World Health Organization, were found from the samples in both 2003 and 2004. The presence of Microcystis spp. in water samples was confirmed through standard polymerase chain reaction (PCR) using a combination of four primer sets. Quantification of Microcystis was accomplished by a real-time PCR assay utilizing specific primer-Taq-man probe sets targeted on a conserved, Microcystis-specific 16S rDNA fragment and a microcystin toxin synthetase gene mcyD. This approach allowed us to specifically study the distribution and abundance of toxic Microcystis in the lake in contrast to previous studies that have assessed Microcystis populations with less refined methods. On the basis of quantification by quantitative real-time PCR analysis, the total abundance of Microcystis cells in the bloom area varied from 4 x 10(8) to 2 x 10(3) cells L(-1). The results of this study provide novel insight regarding the distribution and abundance of Microcystis spp. in the western basin of Lake Erie, a region plagued in recent years by large-scale (>20 km2) blooms. Our results suggest that the Maumee River and Bay may serve as a source for Microcystis to western and central Lake Erie.