The Terrestrial Zoology department of the Western Australian Museum maintains large collections of a wide variety of terrestrial animals, including both terrestrial invertebrates and vertebrates, as well as marine mammals.
The Aquatic Zoology department is responsible for documenting and researching most of the marine, estuarine and freshwater faunal groups of Western Australia, and in some groups a terrestrial component as well.
The Maritime Archaeology department, based in the WA Shipwrecks Museum, primarily researches shipwreck archaeology from the Western Australian coast.
The Earth and Planetary Sciences department maintains, researches and documents six Earth Science collections comprising of Fossils (invertebrate, vertebrate, plant and trace fossils), Minerals, Rocks, Gems, Meteorites and Tektites, totalling more
The Museum’s History department was established in 1970 – the first history department in a state museum in Australia.
Maritime History specialises in collections of images and artefacts representing the individuals, communities, and organisations that contribute to the maritime history and heritage of Western Australia.
The Anthropology and Archaeology department specialises in cultural anthropology and archaeology.