Antarctica has the greatest diversity of lake types on the planet including freshwater, brackish, saline and hypersaline systems, epishelf lakes, ice shelf lakes and lakes and cryoconite holes on glacier surfaces. Beneath the continental ice sheet, there are hundreds of subglacial lakes. These systems are dominated by microbial food webs, with few or no metazoans. They are subject to continuous cold, low annual levels of photosynthetically active radiation and little or no allochthonous nutrient inputs from their catchments. Subglacial lakes function in darkness. Heterotrophic bacteria are a conspicuous and important component of the simple truncated food webs present. Bacterial abundance and production vary between freshwater and saline lakes, the latter being more productive. The bacterioplankton functions throughout the year, even in the darkness of winter when primary production is curtailed. In more extreme glacial habitats, biomass is even lower with low rates of production during the annual melt season. Inter-annual variation appears to be a characteristic of bacterial production in lakes. The factors that control production appear to be phosphorus limitation and grazing by heterotrophic and mixotrophic flagellate protozoa. The evidence suggests high rates of viral infection in bacteria and consequent viral lysis, resulting in significant carbon recycling, which undoubtedly supports bacterial growth in winter. The biodiversity of lacustrine Antarctic heterotrophic bacteria is still relatively poorly researched. However, most of the main phyla are represented and some patterns are beginning to emerge. One of the major problems is that data for heterotrophic bacteria are confined to a few regions served by well-resourced research stations, such as the McMurdo Dry Valleys, the Vestfold Hills and Signy Island. A more holistic multidisciplinary approach is needed to provide a detailed understanding of the functioning, biodiversity and evolution of these communities. This is particularly important as Antarctic lakes are regarded as sentinels of climate change.