A floristic and taxonomic survey was made of the diatom communities of sediments and microbial mats in 66 freshwater and saline lakes and pools in the Larsemann Hills, Rauer Islands and Bølingen Islands (continental eastern Antarctica). A total of 31 taxa were distinguished, 10 of which could not be identified to species (nine) or even generic (one) level, either because they have most probably not yet been described or because they belong to species complexes that are in need of revision. Four new combinations are proposed; three species are reported for the first time from continental Antarctica, while another three are confirmed for eastern Antarctica for the first time. Analysis of literature data on Antarctic lacustrine diatoms shows that taxonomic practice has a profound influence on the assessment of distribution patterns. Force-fitting of European and North American names to Antarctic taxa and erroneous identifications have contributed to an underestimation of endemism in the diatom flora of Antarctic inland waters. In addition, changing concepts on species boundaries during the last decade influence the interpretation of biogeographic patterns. The application of a more fine grained taxonomy will almost certainly reveal a higher degree of endemism in Antarctica, and especially continental Antarctica. The present case study shows that in the Larsemann Hills Antarctic endemics account for about 40% of all freshwater and brackish taxa, while the biogeographic distribution of about 26% is unknown, mainly due to their uncertain taxonomic identity. This contradicts the view that cosmopolitanism prevails in Antarctic diatoms.