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Diatoms are important ecological indicators in Antarctica, and paleolimnologists routinely apply transfer functions to fossil diatoms recovered from lake sediments to reconstruct past environments. However, living diatom communities may differ among the possible habitat types represented in sediment cores (both within lakes and their immediate proximity), hindering the full and accurate interpretation of fossil records. Therefore, an improved understanding of Antarctic diatom habitat preferences would substantially aid in interpreting regional paleo-material. To gain insights into habitat differences, we sampled epipelon, epilithon, Nostoc mats, lake-adjacent moss, and wet soil from > 30 lakes and ponds from Clearwater Mesa, James Ross Island, spanning a broad gradient in conductivity (a common basis for transfer functions). We found that diatom communities significantly differed between habitat types (although abundances were too low in Nostoc mats to characterize communities), with the clearest distinctions being between submerged (epipelon and epilithon) and exposed (moss and wet soil) groups. Submerged habitat types had greater abundances of attached aquatic taxa (i.e. Gomphonema spp.), while exposed habitats harboured more abundant aerophilic genera (e.g. Hantzschia, Luticola, and Pinnularia). Furthermore, only epilithon communities were significantly related to conductivity, and both epipelon and epilithon habitats showed conspicuous increases in Denticula jamesrossensis at greater conductivity values. Collectively, these results improve our knowledge of limno-terrestrial diatoms from the Maritime Antarctic Region, and further highlight the utility of incorporating knowledge of habitat preferences into (paleo)ecological research.