The Philippines' rainforests and its extensive coastlines make it home to a diverse range of birds, plants, animals, and sea creatures. It is one of the ten most biologically megadiverse countries and is at or near the top in terms of biodiversity per unit area.

Around 1,100 land vertebrate species can be found in the Philippines including over 100 mammal species and 170 bird species not thought to exist elsewhere. The Philippines has among the highest rates of discovery in the world with sixteen new species of mammals discovered in the last ten years. Because of this, the rate of endemism for the Philippines has risen and likely will continue to rise.

The Philippines lacks large predators, with the exception of snakes, such as pythons and cobras, saltwater crocodiles and birds of prey, such as the national bird, known as the Philippine Eagle, which scientists suggest as the largest eagle in the world. The largest crocodile in captivity was captured in the southern island of Mindanao. Other native animals include the palm civet cat, the dugong, and the Philippine tarsier associated with Bohol. With an estimated 13,500 plant species in the country, 3,200 of which are unique to the islands, Philippine rainforests boast an array of flora, including many rare types of orchids and rafflesia.

Philippine maritime waters encompass as much as 2,200,000 square kilometers producing unique and diverse marine life and are an important part of the Coral Triangle. The total number of corals and marine fish species was estimated at 500 and 2,400 respectively. However, new records and species discoveries continuously increase these numbers underlining the uniqueness of the marine resources in the Philippines. The Tubbataha Reef in the Sulu Sea was declared a World Heritage Site in 1993. Philippine waters also sustain the cultivation of pearls, crabs, and seaweeds.

Deforestation, often the result of illegal logging, is an acute problem in the Philippines. Forest cover declined from 70% of the country's total land area in 1900 to about 18.3% in 1999. Many species are endangered and scientists say that Southeast Asia, which the Philippines is part of, faces a catastrophic extinction rate of 20% by the end of the 21st century.

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