The Holocene diatom flora identified in three sediment cores from marine bays in the Windmill Islands (East Antarctica) is described and depicted for the first time. One hundred and twenty-four diatom taxa could be identified of which eighty-one taxa have a circum-Antarctic distribution. All taxa are listed in a table together with appropriate references and remarks on ecology and biogeography. The most diverse genera are Fragilariopsis, Navicula and Thalassiosira. Some taxa (e.g., Chaetoceros spp., Fragilariopsis curta, F. cylindrus, Navicula glaciei and Synedropsis spp.) have the potential to be used as indicator taxa for the reconstruction of palaeoceanographic conditions in the Windmill Islands.