Antarctic biota evolved under the influence of a suite of geological and climatic factors, including geographic isolation of the landmass and continental shelves, extremely low temperatures and seasonality. Current warming trends in the continent and surrounding oceans may trigger substantial shifts in community composition and biodiversity, impacting the dominance of cold-adapted over more generalist species. Until recently, the diversity of microorganisms in cold environments was investigated only in terms of distribution, with little attention to their functional roles in important environmental processes. The 'omic' methodologies now offer effective tools to investigate the relationships between biodiversity and ecosystem functioning and to understand the evolutionary principles of adaptation and tolerance/resistance to extreme conditions. In this review we summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies.