Contamination of drinking water sources by cyanotoxins, including microcystins (MCs), nodularins (NOD), cylin-rospermopsin (CYN), anatoxin-a (ANA), homoanatoxin-a (HANA) and beta-N-methylamino-L-alanine (BMAA), produced during harmful algal blooms is a serious threat to human health. The detection, quantitation, and monitoring of cyanotoxins is essential to ensure public safety. A variety of indirect methods including enzyme-linked immunosorbent assay (ELISA), antibody-based techniques, and molecular approaches are available for cyanotoxin detection. While robust and simple, the indirect methods often lack selectivity and sensitivity. Direct detection using chromatographic techniques coupled to a mass spectrometer provide excellent selectivity and sensitivity, but require costly equipment and skilled operation. Matrix-assisted laser desorption ionization time of flight mass spectrometry coupled to a bioaccumulator, toxin chemical derivatization, electrochemical immunosensors, quantitative polymerase chain reaction of toxigenic genes, and specific aptamer recognition have also been demonstrated for cyanotoxin analysis.