Toxic cyanobacteria are known to produce cyanotoxins, toxic secondary metabolites. In recent years the cylindrospermopsin (tricyclic guanidinyl hydroxymethyluracil)-producing organisms Aphanizomenon ovalisporum, Cylindrospermopsis raciborskii, and Umezakia natans have been inhabiting polluted fresh waters. Cylindrospermopsin, a potent hepatotoxic cyanotoxin, has been implicated in cases of human poisoning as well. This study describes the isolation and purification of cylindrospermopsin from A. ovalisporum with the help of a slightly modified Blue-Green Sinapis Test, a plant test suitable for determining the cyanotoxin content of chromatographic fractions besides plankton samples. The recent modification, using microtiter plates for the assay, improves the method and reduces the amount of sample needed for the assay. This approach proved that plant growth and metabolism, at least in the case of etiolated Sinapis alba seedlings, are inhibited by cylindrospermopsin. The establishment of capillary electrophoresis of cylindrospermopsin and consideration of the results reported here lead us to the expectation that capillary electrophoresis of cylindrospermopsin may be a powerful and useful analytical method for investigating cyanobacterial blooms for potential cylindrospermopsin content and toxicity. Confirmation of chemical identity of the purified compound is performed by UV spectrophotometry, NMR, and MALDI-TOF.