With habitat loss and fragmentation among the greatest threats to biodiversity, a better understanding of the habitat use of keystone species is critical in any conservation management strategy. Aldabra Atoll, in the Seychelles archipelago, has the largest population worldwide of giant tortoises. This endemic species (Aldabrachelys gigantea) could be vulnerable to habitat fragmentation and loss induced by climate change related reduction in rainfall. Here, we assess habitat use and selection by A. gigantea in its natural environment on Aldabra. We quantified the habitat areas of A. gigantea based on the first high-resolution terrestrial habitat map of Aldabra, produced for this purpose using satellite imagery. The resulting map was combined with four years of movement data to assess A. gigantea habitat use and selection at landscape and home range scales. Grassland or ‘tortoise turf’ habitat was most preferred by A. gigantea on Aldabra, at the landscape scale across seasons, followed by open mixed scrub. These two habitats cover only 30 km2 (19.2%) of the surface of the atoll (total area: 155.5 km2). At the home range scale, there was no significant preference shown and habitat was used randomly. Our results suggest that Aldabra’s grassland habitat, despite its small area, is of great importance to A. gigantea. Conservation management actions for A. gigantea on Aldabra and elsewhere should therefore focus on the protection and maintenance of this habitat.