Seychelles is among the world's leading countries to protect lands for threatened species, allocating 42% of its territory for conservation. Like many fragile island ecosystems, Seychelles saw the loss of biodiversity when humans first settled in the area, including the disappearance of most of the giant tortoises from the granitic islands, the felling of coastal and mid-level forests, and the extinction of species such as the chestnut flanked white eye, the Seychelles parakeet, and the saltwater crocodile. However, extinctions were far fewer than on islands such as Mauritius or Hawaii, partly due to a shorter period of human occupation (since 1770). Seychelles today is known for success stories in protecting its flora and fauna. The rare Seychelles black parrot, the national bird of the country, is now protected.

The granitic islands of Seychelles are home to about 75 endemic plant species, with a further 25 or so species in the Aldabra group. Particularly well-known is the coco de mer, a species of palm that grows only on the islands of Praslin and neighbouring Curieuse. Sometimes nicknamed the "love nut" because the shape of its "double" coconut resembles buttocks, the coco-de-mer produces the world's heaviest seed. The jellyfish tree is to be found in only a few locations on Mahe. This strange and ancient plant in a genus of its own ("Medusagyne") seems to reproduce only in cultivation and not in the wild. Other unique plant species include Wright's gardenia ("Rothmannia annae") found only on Aride Island Special Reserve.

The freshwater crab genus "Seychellum" is endemic to the granitic Seychelles, and a further 26 species of crabs and five species of hermit crabs live on the islands.

The Aldabra giant tortoise now populates many of the islands of Seychelles; the Aldabra population is the largest remaining. These unique reptiles can be found even in captive herds. The granitic islands of Seychelles may support distinct species of Seychelles giant tortoises; the status of the different populations is currently unclear.

There are several unique species of orchid on the islands.

Seychelles hosts some of the largest seabird colonies in the world, notably on the outer islands of Aldabra and Cosmoledo. In granitic Seychelles the largest colonies are on Aride Island including the world's largest numbers of two species. Sooty terns also breed on the islands. Other birds include Cattle egrets ("Bubulcus ibis") and Fairy terns ("Gygis alba").

The marine life around the islands, especially the more remote coral islands, can be spectacular. More than 1,000 species of fish have been recorded.

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