Antarctica is arguably the world's most important continent for influencing the Earth's climate and ocean ecosystem function. The unique physico-chemical properties of the Southern Ocean enable high levels of microbial primary production to occur. This not only forms the base of a significant fraction of the global oceanic food web, but leads to the sequestration of anthropogenic CO(2) and its transport to marine sediments, thereby removing it from the atmosphere; the Southern Ocean accounts for ~30% of global ocean uptake of CO(2) despite representing ~10% of the total surface area of the global ocean.The Antarctic continent itself harbors some liquid water, including a remarkably diverse range of surface and subglacial lakes. Being one of the remaining natural frontiers, Antarctica delivers the paradox of needing to be protected from disturbance while requiring scientific endeavour to discover what is indigenous and learn how best to protect it. Moreover, like many natural environments on Earth, in Antarctica microorganisms dominate the genetic pool and biomass of the colonizable niches and play the key roles in maintaining proper ecosystem function. This review puts into perspective insight that has been and can be gained about Antarctica's aquatic microbiota by using molecular biology, and in particular, metagenomic approaches. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.