A French Baroque palace built by Grand Master Antonio Manoel de Vilhena, after who the museum was named, the National Museum of Natural History in Mdina, features plants, fossils, minerals, insects, stuffed birds, mammals, skeletons, reptiles, and fishes commonly found in the Malta Islands. Although the exteriors of the museum are well-organized and planned, its interiors are irregular and unbalanced, and this sharp contrast does not go unnoticed.

While a majority of first floor of the museum showcases the marine ecosystem, the room at the end on this floor can send chill down the spines of some with its collection of human skeletons and skulls of Homo erectus pekinensis, Australopithecus boisei, Homo habilis, and other extinct hominids. It also features the skull of a Neanderthal man, complete with a reconstruction of facial features. The second floor houses a vast collection of birds and their eggs. With fantastically preserved specimens, this museum is a must-see for those whose interests lie in the flora and fauna or rocks and minerals.