The island of Giannutri is of calcareous nature and it has been affected in the past by fires that caused vegetation degradation. The presence of submerged and semi-submerged cavities is significant along the limestone coasts of the island. The Posidonia oceanica meadow is well-developed in the eastern part and in some western bays. The island hosts rare marine bird species, also associated with rocky habitats and Mediterranean garigues; moreover, it is an important resting area for migratory birds. The low population density has contributed to preserving the high biodiversity of marine ecosystems. Extensive populations of Cystoseira spp. are present, while some important formations of Lithophyllum byssoides can be found in some parts of the island. The coralligenous habitat characterizes the deeper cliffs with well-structured populations and the presence of yellow gorgonian, red gorgonian, white gorgonian, and red coral. The system of submerged cavities in Giannutri is the largest in Tuscany and it is one of the largest in Italy.