The application of genomic approaches to marine biota has profoundly altered our understanding of life in the oceans, especially regarding concepts of adaptation, speciation and evolution. The avalanche of genomic data has provided an unbiased view of marine biology that has never been seen before. In particular, comparative and metagenomic approaches with microbes from different biogeochemical marine provinces provided the first insights into how they acquire and discard genes as needed, even across kingdom boundaries, in response to their environment. These data clearly reveal that marine microbes have remarkable abilities to change their genomes according to both environmental stresses and biotic interactions. Thus, it is most likely that the flux of energy and matter in the marine system is reflected by the presence or absence of genes and proteins in marine organisms, which could provide novel tools to understand biogeochemical processes of global significance. However, the challenge is to put the reductionistic knowledge gained by genomics and metagenomics into the larger contexts of cellular systems and ecosystems to identify emergent properties that could not have been predicted by breaking down the whole into its individual parts.