Increasing interest in the ecological roles, conservation and biotechnological potential of Antarctic microbiota has focused attention on their biodiversity and evolutionary origins. Antarctic microbial ecosystems provide useful models for general questions in evolutionary ecology given the relative isolation of the South Polar Region, the severe biological constraints imposed by the polar environment, and the absence of higher plants and animals in some Antarctic habitats. Sealed environments such as Lake Vostok and the overlying East Antarctic ice sheet provide unique, natural culture collections for studying microorganisms that have been isolated from the global gene pool over timescales of evolutionary significance. Most Antarctic environments, however, continue to receive microbial propagules from outside the region, as indicated by spore trap data, the microflora found in Antarctic snow and ice, the colonising taxa at geothermal sites, and the high frequency of apparently cosmopolitan species in most habitats. Differences in environmental stability and selection pressure among environments are likely to influence the degree of adaptive radiation and microbial endemism. The latter seems greater in the Southern Ocean by comparison with non-marine ecosystems of Antarctica, although there is some evidence of endemic species in highly specialised niches on the continent such as in the endolithic habitat and saline lakes. Analytical techniques such as 16S rDNA sequencing and DNA–DNA hybridisation are beginning to provide new insights into the genetic affinities and biodiversity of Antarctic microbiota, and are leading to a more rigorous evaluation of microbial endemism.