Astypalaia has been recognized by the scientific community as an ecologically important area, as it hosts many rare species of flora and fauna. The eastern part of the island and the cluster of around 12 islands (Kounoupi, Ofidousa, Koutsomitis, Tigani, Moni, Fteno, Chondropoulos, Fokionisia, Logno, Chondri, Agia Kyriaki and Pontikousa) with 476.5ha area, is included in the NATURA 2000 network (Code GR4210009) and designated as CORINE biotope, among the 39 of the South Aegean Region.
The terrain is mostly mountainous and hilly, with limestone and flysch being the main contents. The coastline of Astypalea is steep and manifold, forming numerous of bays, coves and inlets. In Astypalaia there are two interesting caves: The Negro cave near the Vatses beach, which is associated with stories about pirates and treasures, and the Drakos Cave, in the northeastern part, which features spectacular stalactites and stalagmites and, according to tradition, was a pirate haven.
As regards the vegetation, the island is the home of all the endemic plants of the Aegean, such as Anthemis scopulorum, Arenaria aegaea, Campanula laciniata, Dianthus cinnammeus, Fibigia lunarioides, as well as other rare species such as Aristolochia parviflora, Carum multiflorum, Convolvulus scamonia, Linum arboretum e.t.c.
The vegetation in the eastern part of Astypalaia is characterized by junipers, lentisk and sparse brushwood. The western part is dominated by brushwood species (Obscure, astivi, galazastivi), while around the torrents, osier, oleanders and fig trees are very common. Along the seaside, especially at Livadia, olive trees, fig trees and conifers, reeds and vines are dominating. The presence of aromatic - medicinal plants are interwoven with the landscape of Astypalaia and the intense aromas of native vegetation enchants the visitors.
In the mountains of Astypalea wild and rare plant “crocus” grows. Being collected every November, its stamens called “saffron” are used in local cooking and pastry. In the sea area, an aquatic plant creates underwater meadows which enrich the water with oxygen. Mediterranean seals live in the caves of Astypalaia and the surrounding islands, while in the greater sea area bottlenose dolphin (Tursiops truncatus), striped dolphin (Stenella caeruleoalba), the prasinochelona (Chelonia mydas) and thalassochelona (Caretta caretta) have been observed.
In the surrounding islets rare Aegean birds such as Artemis, the Falcon and the Shag are nesting. Also three species of lizards are found: Gecko (Hemidactylus turcicus), Ofisops (Ophisops elegans) and Silivouti (Podarcis erhardii) and 5 species of mammals (Kipomygalida, rabbits, Hare, Mafropontikos, Spitopontikos).
Various human activities and actions such as fires, intense fishing, hunting and continuous construction threaten both terrestrial and marine organisms.