With the apparent increase in toxic cyanobacterial blooms worldwide, and their resultant impact on human and domestic animal health, it is important to be able to accurately determine the amount of toxin in these blooms. For microcystins, this can be problematic due to the large number of toxin congeners and their variable toxicity. Both activity and structural-based assays exist for the detection of microcystins. Structural-based assays like ELISA, may overestimate the total toxicity in a sample by detecting nontoxic analogues. Currently, several commercial ELISA kits are available for the detection of microcystin, each with its own unique recognition epitope. These ELISA kits were evaluated side by side for their ability to accurately detect microcystin in environmental samples containing a wide range of toxin. In addition, they were compared with the more traditional microcystin detection techniques of HPLC with photodiode array detection (PDA) and the activity-based protein phosphatase inhibition assay (PPIA).