The Terrestrial Vertebrates section of the Museum comprises three complementary but separate collections, Herpetological (amphibians and reptiles), Ornithological (birds) and Mammalian (mammals). More then 42,000 individual specimens are held in these collections, the majority of which are from the Northern Territory. Greatest strengths of the collection are the amphibians and reptiles (73%), though the mammal collection is also highly significant. Though comprehensive, the bird collection has substantial gaps in representation.

Historical collections include the Arid Zone Collection and the Finlayson Mammal Collection. The section can provide expert identification of amphibians, reptiles, birds and mammals, loans and exchanges of specimens to workers at approved Institutions, as well as limited research facilities.

Research activities focus on the taxonomy and systematics of scincid lizards, which are the most speciose group of reptiles in Australia. Research is also carried out on other northern Australian amphibians and reptiles.