The Natural History Museum in Thiruvananthapuram is housed in a spacious, modern, double-storeyed building at the eastern end of the Napier Museum and zoo complex within the museum premises. This museum was established with the personnel collection of minerals and books presented by General Cullen in 1885. The varied and rich collections are now on display at this new building built in 1964.

The museum has separate galleries displaying stuffed mammals, birds, lower vertebrates and invertebrates. The exhibits of fossil tree trunks near the entrance are another big draw. There is an art collection that highlight Kerala's rich heritage in stone, wood and metal sculpture. There are index collections, a skeleton gallery and laboratory. Besides these archeological and cultural specimens, this museum has an excellent ethnographic collection. This includes implements and models of the various communities, primarily of South-India. Replicas of traditional houses (Tharawad) and customs of the communities of Kerala are exclusive exhibits at the Natural History Museum.