Several blooms of Microcystis aeruginosa have been observed in the Patos Lagoon estuary during the last fifteen years without a proper investigation of their ecological importance or possible toxicity. The present study has identified and quantified the presence of cyanobacteria in the Patos Lagoon estuary, particularly of M. aeruginosa. During this survey, identification and quantification of the main phytoplankton groups were done in relation to geographical distribution in the estuary. The presence of M. aeruginosa colonies in the estuarine region confirmed their superficial distribution throughout the estuarine waters during twelve months with a maximum of 1, 3.10(6) cells. L-1 in December, 1994 and a minimum of 1, 5.10(5) cells. L-1 in August, 1995 and also confirmed that M. aeruginosa originated from waters in the north of the estuary. The period of the highest cell and colonies densities was coincident with high chlorophyll-a levels in surface waters. Toxicity of M. aeruginosa bloom material was determined by bioassay and concentrations of hepatotoxins microcystins were identified by HPLC-DAD. M. aeruginosa blooms were considered highly toxic, presenting a 24 h-LD50 lower than 100 mg.Kg-1 b.w. and a toxin content higher than 1 microgram.mg-1 d.w. Several microcystin variants were found in the extracts with microcystin-LR predominating.