The most commonly preserved materials animals leave behind when they decompose are their skeletons, in the form of shells and bones. These materials are used in the field of zooarchaeology, or the study of animal remains from archaeological context, which aims to understand how past peoples interacted with their environment. 

The Zooarchaeological Reference Collection (formerly referred to as Osteological Reference Collection) is a non-excavated collection established and maintained by the division with the purpose of aiding researchers in identifying and interpreting animal remains excavated from archaeological sites. Less than half of the collection are shells or malacological references and the rest are bones of fishes, amphibians, reptiles, birds, and mammals. Majority of the bone collection are from mammals, although a significant number of birds and fishes also comprises a bulk of it.

Among the first materials of the collection are a few skeletal elements like the skull, long bones and flat bones of mammals donated by the Zoology Division of the National Museum of the Philippines in 1978. In the 1980s, the number of items in the collection rapidly increased due to the acquisition of several specimens from fieldworks conducted in Ilocos Sur, Cagayan Valley, Palawan, Mindoro, and Bohol. Foreign animal collections, such as lion, rhinoceros, ibex, giraffe, ostrich, and camel were also acquired in the same decade through the donations of Manila Zoological and Botanical Garden. 

In 1986, during the re-organization of the National Museum of the Philippines, the Archaeology Division was separated from the Anthropology Division and the “Osteological Unit” was changed into the Zooarchaeology Section, which came from zoologico-archaeology concept (John Lubbock 1865), defined by Olsen in 1977 as “the study of the animal remains from archaeological sites and their relationship to humans” (Bautista, n.d.). The establishment and enhancement of the Zooarchaeology Section was also in response to the “growing interest on animal remains by archaeologists and prehistorians in reconstructing the past” (Bautista, n.d.).  The name was proposed by Mr. Angel Bautista who founded the section and developed it further through conducting and publishing researches on faunal remains from archaeological sites. Since then, the collections maintained by the section expanded to include faunal remains from archaeological excavations.