The analysis of a sample taken in a lava tube cave on Île Amsterdam (southern Indian Ocean) revealed the presence of three interesting small-celled naviculoid diatom taxa. Based on light and detailed scanning electron microscopy, two of these taxa are described as new: Mayamaea cavernicola sp. nov. and Sellaphora barae sp. nov. A third taxon, Chamaepinnularia aerophila Van de Vijver et Beyens, was previously only found in the type locality on the nearby Crozet Archipelago. The three taxa are compared to other morphologically similar species from Europe, South America and the (sub-)Antarctic Region.