The occurrence of toxic cyanobacterial blooms in aquatic environments, associated with human health problems and animal deaths, has increased the need for rapid, reliable and sensitive methods to determine the toxicity of microcystin produced by cyanobacteria. An in vitro Microtox® system and a commercially available microcystin ELISA were used to screen out the potential risk associated with selected Microcystis aeruginosa strains (Ma1D–Ma8D). Results showed the existence of three differentiated groups in the selected M. aeruginosa strains. Strains Ma7D and Ma6D were determined to be very toxic, strains Ma2D, Ma1D and Ma5D as moderately toxic and strains Ma8D, Ma4D and MA3D as non-toxic. These results agreed with the microcystin concentration values obtained by immunoassay. Although the data obtained by other authors clearly show that Microtox® is not sensitive to microcystins, our results suggested that this bioluminescence assay may prove useful in the preliminary screening of cyanobacterial blooms for microcystin-based toxicity. Additionally, the combination of immunodetection and toxicity-based Microtox® provides a useful addition to the methods already available for detection of cyanobacterial toxins.