The diverse ecosystems protected within the Podocarpus National park support a rich and varied avifauna. To date over 500 bird species have been recorded in and around the park. Since only the Cajanuma and Las Palmas areas have been adequately surveyed, the list could rise to somewhere between 600 to 800 species, making the Podocarpus National Park one of the most species rich national parks in the world.

The Park protects viable populations of threatened species, such as Golden-plumed Parakeet, White-breasted Parakeet, Red-faced parrot and the Bearded Guan.

The Park also supports populations of several large mammal species, threatened or endangered throughout their ranges, including Mountain Tapir, Giant Armadillo, Northern Pudu Deer, Ocelot, Spectacled Bear and Jaguar.

Podocarpus National Park has immense botanical value. The number of vascular plant species has been estimated to be between 3,000 and 4,000, making the National Park the richest cloud forest, in terms of tree species, in Ecuador.