The faunal diversity in the PPSRNP is moderate with 254 terrestrial vertebrate species recorded., especially with respect to invertebrates. A total of 165 species of birds was recorded in PPSRNP representing 67% of the total bird species of Palawan. It is inhabited by 5 internationally threatened bird species including the Philippine cockatoo (Cacatua haematuropygia) and the Palawan peacock pheasant (Polyplectron emphanum),

There are also some 30 mammal species that have been recorded in the Park. Mammal species include the Park are Bearcat (Arctictis binturong), , the Palawan porcupine (Hystrix pumilus) and the long-tailed macaque (Macaca fascicularis). Also notable are 8 species of bats that inhabit the

There are 19 species of reptiles have been identified in the PPSRNP, of which 8 species are endemic. Reptiles species in the area include large predators like the Common reticulated python (Phython reticulatus), the Monitor lizard (Varanus salvator), and rare fresh water turtles (Caura ambionensis).

Amphibians are the smallest group of vertebrates with only 10 species identified. Most dominant and frequently encountered is the Philippine woodland frog (Rana acanthi), one species, Barbourula busuangensis, endemic to Palawan was also observed in the area.

Invertebrate species are principally represented by insect fauna. Of insects surveyed, the Lepidoptera group that include species like Trojana are the most commonly observed. The subterranean river is home to creatures that include Megalomorph spider, Thereupoda, and Amblypygius or tailess whip scorpion.

In the marine component, Green sea turtle (Chelonia mydas) and Hawksbill turtle (Eretmochelys imbricate), both internationally endangered species are also observed to nest in the white sand beaches and feed in the sea grass beds dominated by tropical eelgrass (Enhalus acoroides)  species. Commonly seen species are the Horned starfish, Spotted sea cucumber, and Cigar wrasse.