The Fauna survey team conducted its reconnaissance survey in seven barangays, namely: Mt. Salakot, Barangay Napsan, Barangay Simpocan, Barangay Nagtabon, Barangay Langogan, Barangay Bahile, Barangay Irawan, and Barangay Iwahig. Several sampling sites were selected in each 7 barangays where transects were established. The selected sampling sites are more or less the same with the sampling sites of the Flora team for consistency purposes.

The Fauna team was able to identify a total of 135 species in 63 families and 19 orders.  The 11 amphibians are distributed in 4 families and 1 order, and the 7 reptiles in 6 families in 1 order and 2 sub-orders. Ninety-four species of birds are distributed in 40 families and 10 orders while the 23 mammals in 13 families and 7 orders. The top 4 barangays which registered the highest species count are: Langogan (67), Bahile (67), Napsan (64), and Irawan (61). 

Mammal species diversity and richness, have the following highest ranked areas: Napsan (H’ =0.467,  R = 3.74), Simpokan (H’ = 0.402, R = 3.33),  Langogan  (H’ = 0.259, R = 1.31)  and Bahile (H’ = 0.178, R =1.52).  The relative ranks for bird species diversity and richness show  Bahile ( H’ = 1.57, R = 3.61) having  the highest  value followed by Irawan (H’ = 1.51, R = 3.78), Langogan (H’ =1.49, R = 3.59), Napsan (H’  = 1.44, R = 3.30) and Bacungan (H’ =1.42, R = 3.60). Reptile diversity and richness are all low, but the ranking of the highest are as follows: Bacungan (H’-0.439, R- 0.83), Bahile and Irawan, having both H’ = 0.30, R = 1.41, Langogan and Simpokan  with H’ = 0.217, R = 1.512). Amphibian species diversity and richness show Simpokan (H’ = 0.5008, R =0.84),  Bahile (H’ = 0.4000, R = 1.15), Irawan (H’ =0.468, R = 0.657),  Bacungan (H’= 0.346, R = 0.530) as the top barangays.

In terms of overall species richness, the following barangays: Bahile, Simpokan, Napsan and Langogan. Species diversity in all sampling sites was relatively low with less than 2.5 index value.

Puerto Princesa has 33% of the total count of Palawan endemics. Amphibians have the highest endemicity at 45% (5 species); birds registered 34% (32 species) and mammals posted 35% (8 species). The level of endemism by barangay is as follows starting from the highest: Napsan - 47% (30 species); Irawan - 43% (26 species); Langogan – 35% (24 species); Simpukan -38% (18 species); Montible – 38% (13 species); and Bahile – 29% (20 species). 

About 45% of the number of threatened species in Palawan (i.e., 38 species) is found in Puerto Princesa (i.e., 17 species). Of the total number of threatened species in Puerto Princesa City, mammals registered the highest with 30% or 7 species, followed by reptiles with 14% or one species, birds with 9% or 8 species, and amphibians with 9% or one species.  Table II.10 shows the ranking of barangays in terms of the number of threatened species.

The Flagship species are those which are locally endemic and/or threatened, and/or rare in the Philippines and found only in Palawan. In Puerto Princesa the flagship species consist of 10 mammal species, 47 birds, 1 reptile and 5 amphibians. Overall, Napsan has the greatest number of flagship species (42) followed by Irawan (34), Bahile (29), Simpukan (28), Iwahig (22), Nagtabon (17), and Langogan (13). This presence of flagship species is also an important factor for determining the importance of a site as a core zone or a buffer zone.