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The diatom flora of three lakes in the ice-free Amery Oasis, East Antarctica, was studied. Two of the lakes are meltwater reservoirs, Terrasovoje Lake (31 m depth) and Radok Lake (362 m depth), while Beaver Lake (>435 m depth) is an epishelf lake. The lakes can be characterized as cold, ultra-oligotrophic and alkaline, displaying moderate (Radok and Terrasovoje lakes) to high (Beaver Lake) conductivities. There was no diatom phytoplankton present in any of the three lakes. While 34 benthic diatom taxa were identified from modern and Holocene sediments of Terrasovoje and Radok lakes, a 30-cm long sediment core recovered in Beaver Lake was barren. Five species (Luticola muticopsis, Muelleria peraustralis, Pinnularia cymatopleura, Psammothidium metakryophilum, P. stauroneioides) are endemic to the Antarctic region. All identified taxa are photographically documented and brief notes on their taxonomy, biogeography and ecology are provided. The most abundant diatom taxa are Amphora veneta, Craticula cf. molesta, Diadesmis spp, M. peraustralis and Stauroneis anceps. This is the first report on the diatom flora in lakes of the Amery Oasis.