During an extensive survey of the freshwater and moss-inhabiting diatoms of the Prince Edward Islands, a total of 214 taxa belonging to 60 genera were found. Three main communities can be found on the two islands. A large part of the samples was grouped into an aquatic group, bringing together all samples from lentic and lotic waterbodies. A second, contrasting, group was formed by all dry samples whereas in a third group all habitats with higher mineral contents were found. The habitats differed clearly in taxa composition reflecting that way possible environmental differences. Although the diatom composition between the two islands of this island group (Marion and Prince Edward Island) showed some minor qualitative differences, no marked quantitative differences have been observed. The diatom flora shows a distinct similarity with the other islands in the southern Indian Ocean, such as the Crozet archipelago and the Kerguelen Islands forming a biogeographical entity in this part of the ocean, distinctly separated from the non-marine diatom flora in other parts of the (sub-)Antarctic Region.