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Most cooperation between Canada and the EU in fisheries matters takes place in the context of Regional Fisheries Management Organizations (RFMOs), particularly the Northwest Atlantic Fisheries Organization (NAFO). The EU and Canada are founding members of NAFO and have worked together closely to bring about major reforms to this organisation. NAFO has achieved some important milestones by advancing precautionary and ecosystem approaches among its members, strengthening its monitoring, control and surveillance systems, and enhancing the transparency of the organization. As a result, the compliance of fishing vessels with NAFO regulations has visibly increased, illegal, unreported and uncontrolled (IUU) fishing has decreased, and some fish stocks are already showing signs of recovery. However, in spite of the modern approaches to fisheries management, the abundance of many traditional NAFO fish stocks continues to be low, an indication that the rebuilding process will take time.

NAFO also has a joint enforcement scheme, to which Canada and the EU provide most of the inspection presence, entailing close cooperation to coordinate the presence of respective inspection platforms and inspections. Canada and the EU cooperate closely as members of other RFMOs, such as the International Commission for the Conservation of Atlantic Tunas, the North Atlantic Salmon Conservation Organization and the Western and Central Pacific Fisheries Commission.  Canada is also a cooperating non-Contracting Party in the North East Atlantic Fisheries Commission, in which the EU is a member, and a State Party to, but non-Member of, the Convention on the Conservation of Antarctic Marine Living Resources. Both Canada and the EU are cooperating non-Contracting Parties in the Inter-American Tropical Tuna Commission.

Canada and the EU are parties to the UN Convention on the Law of the Sea and to the 1995 UN Agreement on the Conservation and Management of Straddling Fish Stocks and Highly Migratory Fish Stocks. Both also participate in and support efforts through the UN Food and Agriculture Organization (FAO) to deal with various global fisheries and oceans issues, including the global problem of illegal, unregulated and unreported (IUU) fishing, notably the International Plan of Action on IUU Fishing. Canada and the EU are parties to the FAO Agreement to Promote Compliance with International Conservation and Management Measures by Fishing Vessels on the High Seas, and both support the 1995 FAO's Code of Conduct for Responsible Fisheries. Canada and the EU are cooperating regarding the implementation of the United Nations fisheries agreements.

In December 2009, Canada opened a Catch Certification Office to support Canadian exports of fish and seafood products affected by the European Union (EU) regulation establishing measures to address illegal, unreported and unregulated (IUU) fishing and applies to any country exporting fish and seafood products to the EU. The EU regulation went into effect on January 1, 2010.

Annual Canada-EU High Level Meetings, as well as ad hoc issue-specific meetings, have enabled senior officials to exchange views on matters of common interest and ways to improve fisheries relations. Other issues have included discussions on Canada's integrated oceans management as part of the development of an EU maritime policy.

Canada is surrounded by the Arctic, Atlantic and Pacific Oceans and is home to the Great Lakes which translates to one of the world's most valuable commercial fishing industries, worth more than CDN $5 billion a year and providing more than 130,000 jobs to Canadians. In 2008, Canada's fish and seafood exports were valued at $3.9 billion. Canada exports an estimated 80%, by value, of its fish and seafood production. The United States is Canada's largest export market (representing roughly 62% of seafood trade) followed by the European Union (15%), Japan (8%) and China (6%).

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