The cyanobacteria inhabit every illuminated environment on Earth, from polar lakes to desert crusts and through their phototrophic metabolism play essential roles in global geochemical cycles. With the discovery of marine Synechococcus and Prochlorococcus almost 30 years ago, cyanobacteria have now earned their place as dominant primary producers contributing over 25 percent of global photosynthesis. Their global abundance is now explained from the coexistence of ecotypes that occupy different niches along spatial and temporal gradients. New ecotypes of Synechococcus have been identified as abundant components of microbial communities in freshwater environments and marginal seas. Extensive comparative genomics of marine and freshwater picocyanobacteria have begun to unmask adaptations to light and nutrient (N, P, Fe) limitation that these diverse environments present. Novel types of cyanobacterial diazotrophy input new N and structure microbial communities in the open sea. Current challenges include the understanding of the interactions between marine cyanobacteria and other microbes in their immediate community. In contrast, mesotrophic and eutrophic environments such as the Laurentian Great Lakes have been increasingly affected by nuisance and toxic cyanobacterial blooms that have yielded severe declines in water quality. Factors promoting bloom formation and the functional roles of toxins are important issues being addressed today.