Animal fossils dominate the National Paleontological Collections.  Of these, the most common fossil fauna are the mollusks found in almost all parts of the Philippines. These fossils reflect the marine origins of the country in terms of its geological history. Due to this fact, marine fossil fauna like coral fragments, sea urchin tests, and shark teeth are also commonly present in many parts of the country.

Fossils from other taxon groups, although small in number, are also part of the national collection. Fish fossils like black marlin and freshwater species were found in Pangasinan and Rizal respectively. Bovid bone and teeth fragments were found in Cebu, Cagayan, and Pangasinan. There are also a few microfossils like the foraminifera Orbitolina sp. from Caramoan and the Cycloclypeus sp. from Cebu. 

The national collection also includes foreign-acquired pieces from different parts of the world. The Larry and Pat Gotuaco Collection includes stunning pieces of colorful ammonite fossils from Madagascar and the USA. These pieces were donated to the National Museum of the Philippines in 2018. Several pieces were collected by the division’s researchers themselves like shark teeth from Chesapeake Bay, Maryland, USA and some leaf imprints from Kobe, Japan.