Microalgae and cyanobacteria are at the base of the aquatic food web, and thus play an important role as food for higher trophic levels, in carbon and oxygen cycling, and in the cycling of nutrients. They are also a rich source in biodiscovery and a very useful tool in biotechnology. However, these species can also be a nuisance or harmful to humans, other organisms, and the aquatic ecosystem when they become very abundant and/or produce phycotoxins. Different species and even different populations within a species may have diverging traits and behavior. Currently we have a limited understanding of microalgae’s genetic and metabolic diversity, how species interact with each other and with the abiotic environment, what drives their secondary metabolite production. These, and related questions are what we address in the CyanoLab at the School of Biology, Aristotle Univeristy of Thessaloniki, Greece.