The change of name from the Department of Fisheries and Wildlife to the Fisheries Department was announced with the Fisheries Amendment Regulations (No. 3) 1986 on 1 August 1986. The new Fisheries Department was tasked with managing fish resources in Western Australia. The Department administered two Commonwealth and five State Acts: Commonwealth Fisheries Act 1952, Continental Shelf (Living Natural Resources) Act 1968, Oyster Fisheries Act 1881, Fisheries Act 1905, Fisheries Adjustment Schemes Act 1987, Pearling Act 1990, Whaling Act 1937.

The Fisheries Department underwent a subsequent name change in November 1997 to become Fisheries Western Australia.
The Department's mission is to manage the fish resources of Western Australia for the benefit of the community.

The Department is concerned with both the commercial fishing industry and recreational fishing interest groups. In addition to major managed commerical fisheries such as rock lobster, pearling, and prawn trawling the Department is also responsible for managing Western Australia's fledgling aquaculture industry.