Alkaloid containing plants represent a heterogeneous group both taxonomically and chemically, a basic nitrogen being the unifying factor for the various classes. As most alkaloids are extremely toxic, organisms containing them do not feature strongly in medicine but they have always been important in the allopathic system. Typical alkaloids are derived from plant sources, they are basic, they contain one or more nitrogen, and they usually have marked physiological actions in humans or other mammalian species. This review will present various alkaloids generated by cyanobacteria, highlighting their complex structures, powerful bioactivities, and pharmacological properties. The main groups of cyanobacterial alkaloids include the neuromuscular transmission blocker anatoxins, the ion channel blocker saxitoxins, the degenerated amino acid β-methylamino-L-alanine, the protein synthesis inhibitor guanidine alkaloid cylindrospermopsins, and cyanobacterial indol alkaloids with antiviral, antifungal, and cytotoxic activity.