The atoll is comprised of four large coral islands which enclose a shallow lagoon; the group of islands is itself surrounded by a coral reef. Due to difficulties of access and the atoll's isolation, Aldabra has been protected from human influence and thus retains some 152,000 giant tortoises, the world's largest population of this reptile.

The least-disturbed large island in the Indian Ocean, Aldabra is of outstanding scientific interest. It is the only place in the world where a reptile is the dominant herbivore; some 150,000 giant tortoises (more than on the Galápagos Islands) feed on tie grasses and shrubbery, including plants that have evolved to take advantage of tortoise grazing patterns. The tortoises are the last survivors of a life form once found on many Indian Ocean islands; slow-moving and vulnerable, the giant land tortoises on all other Indian Ocean islands have been driven to extinction by human exploitation, leaving Aldabra as their only remaining stronghold. The island's isolation has allowed the evolution of a distinct fauna, with two endemic birds (Aldabra arush warbler and Aldabra drongo) and another 11 birds that have distinct subspecies (showing evolution in action); among the most interesting is the Aldabran white-throated rail, the last representative of the western Indian Ocean flightless birds - all others have gone the way of the dodo.