The occurrence of cyanobacterial blooms in nutrients enriched aquatic ecosystems is a widespread phenomenon. Cyanobacterial blooms synthesized several bioactive compounds, and cyanotoxin is among one of them. The most commonly reported cyanotoxin are Nodularin, Microcystins Anatoxin-a, Saxitoxins, and Cylindrospermopsin. Biochemically, cyanotoxins are polyketides, alkaloids, nonribosomal peptides, potent toxins, and trypsin inhibitors. Pharmaceutically and neutraceutically these are significant, and exhibits, a diverse range of bioactivity, mainly antiviral, antibacterial, antitumor, anticancerous, antifungal, etc. Several oligopeptides are synthesized through nonribosomal peptide synthetase (NRPSs) in prokaryotes and lower eukaryotes. Cyanobacterial bioactive compounds are not utilized in growth and developments but are a promising source for the novel compounds. Nutrient composition especially nitrogen and phosphorus significantly influences types of bioactive compounds. The common cyanotoxin frequently occurred in cyanobacterial blooms is Microcystin, and is encoded by mcy gene cluster in freshwater and brackish water ecosystems. There are several methods used for purification and characterizations of the bioactive compounds from blooms forming cyanobacterial such as HPLC, UPLC, LC-MS-MS, and MALDI-TOF-MS. This review mainly focused on novel bioactive compounds obtained from cyanobacteria. © 2023 Scrivener Publishing LLC. All rights reserved.