Prochlorococcus is the numerically dominant cyanobacteria found in the oligotrophic ocean, accounting for 25-50% of primary production in these regions. It has been well established that the distribution of the major clades of Prochlorococcus track light, temperature and other environmental variables, yet the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We pyrosequenced (Roche 454 GS FLX+ Titanium) the ITS region of Prochlorococcus communities isolated from surface waters across spatial and temporal environmental gradients in the Pacific to determine the ecological drivers of population structure and diversity across taxonomic ranks. Basin-scale and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.