Biological degradation of cyanobacterial hepatotoxin microcystins in estuarine and coastal water samples from the Patos Lagoon estuarine system, a coastal lagoon situated at the southernmost region of Brazil, was observed. Samples of natural surface water were spiked with purified and semi-purified microcystins (MC-LR and [D-Leu(1)]MC-LR) and their concentrations were monitored by HPLC analysis. After 15 days, the toxins were no longer detectable and after 43 days less than 90% of the initial concentration added to the samples was detected by ELISA. The average degradation rates and the exponential decay rate constants from inside and outside of the estuary were similar. A microcystin degradative bacterium was isolated from the estuarine region. Partial sequence of the 16S rDNA showed a 96% homology with the Burkholderia genus. This genus belongs to the beta subdivision on proteobacteria. This is the first report showing the genus Burkholderia as a cyanobacterial toxin degrader.