The Ichthyology (Fish) section of MAGNT was established in 1981. It includes over 29,900 lots and about 250,000 specimens; with 69 primary types (holotypes) and 375 secondary types (paratypes).

The collection's emphasis is on the marine, estuarine and freshwater fishes of northern and central Australia, Australia, Southeast Asia, and the Indo-Pacific.

Historical collections include the Arid Zone Collection and the JETINDOFISH voucher collection. The section can provide expert identification of fishes, 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 the great diversity of gobioid fishes - the gobies, gudgeons and mudskippers of the Indo-Pacific. There are about 2,500 species of gobioids (they are a suborder of perch-like fishes), and they comprise at least 10% of all living fishes. Other fish research is carried out on mangrove fishes, coral reef fishes and northern Australian freshwater fishes.