The wildlife of the Philippines includes a significant number of endemic plant and animal species. The country's surrounding waters reportedly have the highest level of marine biodiversity in the world. The Philippines is one of the seventeen megadiverse countries and is a global biodiversity hotspot. In 2013, 700 of the country's 52,177 species were listed as threatened.

The Philippines has among the highest rates of species discovery in the world with 16 new species of mammal discovered in the last ten years. Because of this, the degree of endemism in the Philippines has risen and will likely continue to rise.

Some of the smallest and largest animals and plants are found in the Philippines. These include the smallest primate (tarsier), the biggest moth (Atlas moth, or mariposa in Tagalog), the smallest deer (Philippine mouse-deer or pilandok), the smallest fish (Philippine goby), and the biggest fish (whale shark).

There are 714 species of birds in the Philippines, of which 243 are endemic, three have been introduced by humans, and 52 are rare or accidental occurrences. The Philippines has the third-highest number of endemic birds, behind the much larger countries of Australia and Indonesia. There are 67 globally threatened species, including the rufous hornbill and the critically endangered national bird of the Philippines, the Philippine eagle or monkey-eating eagle. Until 1995, the national bird of the Philippines was the maya (which, in the Philippines, refers to a variety of small, commonly observed passerine bird). The Philippines is also home to Tawi-Tawi's blue-winged racket-tail, the most endangered parrot species in Southeast Asia, the Sulu hornbill, one of the most endangered animals in the world with a population of just 27, and the Calayan rail, the most endangered species of rail in the world, found only on a small island in the Babuyan Islands.

According to the EDGE of Existence Programme of the Zoological Society of London, the Philippines has the highest level of bird endemism in the world. Six of the world's 50 most evolutionary distinct and globally endangered (EDGE) species are found in the Philippines. These species are the Philippine eagle (15th place, the highest from the Philippines), spoon-billed sandpiper (#19), black-hooded coucal (#22), Sulu hornbill (#41), Cebu brown-dove (#46), and rufous-headed hornbill (#50). Previously, in 2013, when the list was up to 100, the various bleeding heart dove species, found only in the Philippines, and the Philippine cockatoo were also on the list.

There are more than 111 species of amphibian and 270 species of reptile in the Philippines, of which 80% and 70% are endemic, respectively. Of the 114 species of snake, it is thought that no more than 14 are venomous. Several species of reptiles and amphibians remains undescribed. The Philippines also has 50–60 endemic Platymantis frog species, making it by far the most diverse genus of amphibians in the archipelago.

The endemic freshwater crocodile Crocodylus mindorensis is critically endangered and is considered the most threatened crocodilian in the world. In 1982, wild populations were estimated to be only 500–1,000 individuals; by 1995 a mere 100 crocodiles remained living in the wild. The recent discovery of a population of this species in the Sierra Madre mountains of Luzon brings new hope for its conservation. Projects are being conducted in an effort to save the crocodiles. The Crocodile Rehabilitation, Observance and Conservation (CROC) Project of the Mabuwaya Foundation is active in carrying out such projects.

Other threatened reptiles include Gray's monitor and the Philippine forest turtle. Of the three species of frugivorous monitor lizards globally, two occur in the Philippines: the Panay monitor lizard from the island of Panay and Northern Sierra Madre forest monitor from north east Luzon.