Dried cyanobacteria ('Spirulina') are sold as a nutraceutical for their high content of proteins, essential fatty acids and vitamins. Beyond spirulina, other genera of cyanobacteria produce interesting small molecules that could find use in nutraceutical or pharmaceutical applications. This account presents recent research efforts on antimalarial nostocarboline and the aerucyclamides, as well as on potent toxins such as cyanopeptolin 1020 and microcystins. Combinations of spectroscopic, computational, chemical and biological studies investigated the mechanism of action of these compounds. Their application potential with regard to nutraceuticals or pharmaceuticals is discussed.