Abstract: This invention is at least one panel of qPCR/RT-qPCR assays which enables simultaneous testing for the presence of multiple species and subgroups of cyanobacteria that produce microcystin, anatoxin, saxitoxin, and cylindrospermopsin cyanotoxins. The method takes into account that some cyanobacteria species may carry genes associated with multiple toxin types. Testing for each toxin type is conducted under standardized test conditions which allow quantification of the number of gene copies present for cyanotoxins which may contribute to the overall toxin level.