Cyanotoxins are produced by the toxic cyanobacterial species present in algal blooms formed in water bodies due to nutrient over-enrichment by human influences and natural environmental conditions. Extensive studies are available on the most widely encountered cyanotoxins, microcystins (MCs) in fresh and brackish water bodies. MC contaminated water poses severe risks to human health, environmental sustainability, and aquatic life. Therefore, commonly occurring MCs should be monitored. Occasionally, detection and quantification of these toxins are difficult due to the unavailability of pure standards. Enzymatic, immunological assays, and analytical techniques like protein phosphatase inhibition assay, enzymelinked immunosorbent assay, high-performance liquid chromatography, liquid chromatography-mass spectrometry, and biosensors are used for their detection and quantification. There is no single method for the detection of all the different types of MCs; therefore, various techniques are often combined to yield reliable results. Biosensor development offered a problem-solving approach in the detection of MCs due to their high accuracy, sensitivity, rapid response, and portability. In this review, an endeavor has been made to uncover emerging techniques used for the detection and quantification of the MCs.