Antarctic terrestrial ecosystems are cold, dry, low nutrient environments, with large temperature fluctuations and paradoxically low levels of water availability. These extreme environments are dominated by microorganisms (viruses, archaea, eubacteria, fungi and microsporidia, alveolata, stramenopila, rhodophyta, green algae and protists), which can either tolerate or are adapted to exploit unfavourable growth conditions. However, climate change is altering the growth environment in Antarctica, and so selection pressures on these microorganisms are changing which, in turn, might affect microbial activity in key processes such as biogeochemical cycling. Although the direct effect of a change in, for example, temperature, is known for very few Antarctic microorganisms, molecular techniques (to monitor population structure) and genomic techniques (to identify specific gene function) are starting to give us an insight into what the potential effects of climate change might be at the cellular level. The key to how microorganisms respond to such change depends upon the rate and magnitude of the change along with the physiological capability of microorganisms to adapt or tolerate those changes. Here we will examine a number of case studies in which the effects of factors such as temperature, nutrient availability, grazing, salinity, seasonal cycle and carbon dioxide concentration have each been demonstrated to affect bacterial community structure in polar and alpine ecosystems. The results suggest that the spatial distribution of genetic variation and, hence, comparative rates of evolution, colonization and extinction are particularly important when considering the response of microbial communities to climate change.