Cyanobacteria (blue-green algae) are undesirable in ponds used to raise fish for human food. Management of cyanobacterial communities in aquaculture ponds has been hindered by the small number of herbicides approved for use in food-fish ponds and by the lack of selectivity toward cyanobacteria for those herbicides that are approved for that use. To facilitate development of additional management options, a rapid bioassay utilizing 96-well cell culture plates was developed for screening herbicides and other phytotoxins for selective toxicity toward cyanobacteria. Oscillatoria cf. chalybea and Selenastrum capricornutum were chosen as representatives of cyanobacteria (Cyanophyta) and green algae (Chlorophyta), respectively. In the bioassay, wells of the cell culture plates were inoculated with cyanobacterial or unialgal culture. One of five herbicides (atrazine, diuron, endothall, fluridone, or paraquat) was then added to the wells at various concentrations, and absorbance (650 nm) was measured at 24-h intervals. Growth of treated cultures relative to untreated cultures was used to determine relative toxicity of the herbicide to the two organisms. Paraquat was the most selective of the herbicides tested and was over 10-fold more toxic to O. cf. chalybea than to S. capricornutum. This method was demonstrated to be a rapid, effective, and highly reproducible bioassay to identify selective algicides.