Microcystin (MC) concentrations in cyanobacterial strains isolated from a freshwater lake and from Microcystis PCC 7806, were quantified by three different immunoassays. Polyclonal antibodies (PAbs) developed by linking the cyanobacterial hepatotoxin MC-LR, via 2-mercaptoethylamine to keyhole limpet hemocyanin and monoclonal antibodies (MAbs) against MC-Leucine/Arginine (LR) (MC10E7) were developed in-house as an ELISA kit, versus a commercial MC-LR enzyme-linked immunosorbent assay (ELISA). Depending on the MC variant used, the immunoassays showed different sensitivities to different variants. Statistical analyses were performed between immunoassays, the response of the ELISA, and MC concentrations in the samples. Overall good agreement was found among the ELISAs with no significant differences in the reaction of the antibodies (MAb, PAb) to the MCs (p >0.05). To a large degree, this finding was due to the cross-reactivity characteristics of the MAbs and PAbs used. High-performance liquid chromatography (HPLC) analysis was conducted to compare with the results obtained by ELISA and to determine the profile of MCs produced by the cyanobacteria.