Cyanobacteria are the first oxygenic photosynthesis performing prokaryotes. They are considered to have fast growth, amenability to genetic modifications towards photo-autotrophy. Have the ability to grow under heterotrophic conditions with minimum available sunlight to obtain energy by utilizing organic carbon as its substrate. Cyanobacteria are diversely spread in marine, freshwater, terrestrial habitats which differ from each other concerning their structural and functional metabolism. It produces bioactive compounds which are toxic to animals as well as humans which are produced in freshwater habitats whereas marine species of cyanobacteria produce secondary metabolites which are involved in the production of new drugs and also show potential in various fields such as Biotechnological applications, pharmacology, agriculture sustainability, and environmental remediation. Cyanobacteria also produce non-toxic compounds which help in protecting plants by producing phytohormones, siderophores, and UV protective or absorbing compounds. Marine cyanobacterial bioactive compounds are involved in several bioactivities such as antiviral, antialgal, antiprotozoal, antifungal activities, etc. Freshwater species are involved in forming harmful cyanobacterial blooms which are highly toxic to animals as well as humans (Ex: cyanotoxins, hepatotoxins, etc). Different strategies are used to detect the cyanobacterial compounds under in-vivo and in-vitro cultures. To analyze the quality and safety of water, screening methods are necessary to detect possible toxic compounds present in the environmental habitats. Screening methods include microscopy assay, physiological methods, chemical methods, biochemical-based methods, and molecular-based methods. All these methods of screening help in characterizing, identifying the cyanobacterial toxins and also have a few limitations in their reliability, sensitivity, and limit in the detection of the compounds.