Geothermal areas, such as volcanoes, might have acted as glacial microrefugia for a wide range of species. The heavily glaciated but volcanically active Antarctic continent presents an ideal system for assessing this hypothesis. Ice-free terrain around volcanoes in Antarctica is, however, often restricted to small patches, whereas subglacial cave systems, formed by vented volcanic steam, can be extensive and interconnected. No observations of macrobiota have yet been made for subglacial geothermal environments in Antarctica, but these organisms are often patchily distributed and can be difficult to find. We carried out metabarcoding (eDNA) analyses of soil samples taken from exposed areas on three volcanoes in Victoria Land, and subglacial caves on Mount Erebus. We found evidence of numerous eukaryotic groups, including mosses, algae, arthropods, oligochaetes and nematodes, at both exposed and subglacial sites. Our findings support the notion that geothermal areas—including subglacial environments—can nurture biodiversity in glaciated regions.