El Nido, being one of the most diverse ecosystem in the country, is protected for its unique flora and fauna, and pristine geologic formations. These include:
- limestone cliffs, the home of the swiftlets
- 50 white sand beaches
- 5 types of forest (the lowland evergreen rainforests found in the mainland and islands such as Miniloc, Lagen and Pangulasian; semi-deciduous forests; forests over limestone; beach forests; and, the mangrove forests found mostly around major rivers and creeks in the mainland)
- 3 major marine habitats
- 16 endemic and 10 threatened species of birds (including the Palawan Hornbill, the Palawan Shama, the Palawan tit, Palawan Scops Owl, and the Palawan Peacock Pheasant)
- 6 species of marine mammals endemic to Palawan (including dolphins and its native dugong)
- the Palawan Tree Shrew, the Palawan Stink Badger, the Palawan Spiny Rat, the Palawan Anteater, and the Northern Palawan Tree Squirrel
- 4 species of endagered marine turtles (hawksbill, olive ridley, leatherback and green sea turtles)
- 100 species of corals, 45 of which belongs to the genera of hard corals
- 813 species of fish
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