Canada's marine fisheries are controlled by the Department of Fisheries and Oceans (DFO). Their mandate is to "maintain marine safety and environment protection, scientific excellence, conservation and sustainable resource use." With over 53,000 commercial fishers and more than 34 harvested species in the Maritimes alone, DFO relies on the recommendations and expertise of other governmental institutions. The Fisheries Resource Conservation Council (FRCC), created in 1993, involves a partnership between scientific and academic experts, and all sectors of the fishing industry. The Council makes public recommendations to the Minister of Fisheries and Oceans on such issues as total allowable catches (TACs) and other conservation measures for the Atlantic fishery. It also advises the Minister on Canada's international position with respect to fish stocks that straddle the 200-mile fishing boundary.

Similarly, the Canadian Stock Assessment Secretariat (CSAS) is involved with the coordination of scientific issues facing the DFO. While each region in Canada conducts their own resource assessment reviews, CSAS facilitates the inter-regional exchange of innovation, interpretation, and insight. CSAS also compiles the results of such reviews, providing status reports on the state of fish stocks and overview documents on issues and ecosystems.

A third organization that assists the DFO is the Standing Committee on Fisheries and Oceans, a specialized, permanent group established through the House of Commons to deal with matters of national importance (ie. the cod moratorium in 1995 and the more recent sealing controversy).

Most species in the marine fishery are subject to a quota system in order to protect sustainable levels. The total allowable catch (TAC) for each species is set annually by the DFO and is based on the principle of "replacement yield," which is defined as the number of animals that can be taken from the population without having it decrease in size.