We present a novel model of marine ecosystems in which a diverse initialized phytoplankton community self-organizes according to relative fitness in the physical, chemical and predatory environment. Community structure and the physiological character of the dominant organisms are emergent properties. Results from idealized onedimensional models and an ensemble of global simulations, coupled to an ocean general circulation model, show plausible and robust phytoplankton biogeography. In a test case the global model successfully reproduces the observed relationships between the physiology and habitats of ecotypes of the cyanobacteria Prochlorococcus. This approach provides a new framework for studies of microbial ecology and genomics and in which to test and examine theories of the relationships between ecology, biogeochemical cycles, variability and climate change.