This study investigates the capability of a Bacillus flexus strain isolated from decayed cyanobacterial blooms for the bioremediation of Cylindrospermopsis raciborskii and cylindrospermopsin (CYN) toxin. The algicidal activity of this strain was tested by co-cultivation with C. raciborskii cultures. CYN biodegradation was investigated in the presence of living and heat-inactivated bacterial cells or bacterial filtrate. Living bacterial cells inhibited C. raciborskii growth after 2 days of incubation with complete cell death at day 5. Bacterial filtrate caused a rapid reduction in C. raciborskii growth at the first day, with complete cell lysis at day 3. Only living cells of SSZ01 caused reduction in CYN released into the medium during the bacterial decay of C. raciborskii cells. The biodegradation rate of CYN by SSZ01 relied on initial toxin concentrations. The highest rate (42 μg CYN L−1 day−1 ) was obtained at the higher initial concentration (300 μg L−1 ), and the lowest (4μg CYN L−1 day−1 ) was at lower concentration (50 μg L−1 ). These results suggest that this bacterial strain could be employed to bioremediate cyanobacterial blooms in freshwaters. Also, the application of this bacterium in slow sand filters would give possibilities for degradation and bioremediation of cyanotoxins in drinking water treatment plants.