Preheat oven to 350 degrees F (175 degrees C). Grease an 8x 12 inch baking dish. Bring a large pot of lightly salted water to a boil. Add cod fillets and cook for 4 to 6 minutes; drain.
Melt margarine in a medium saucepan. Remove from heat and mix in the flour and milk. Return to stove over medium heat, and stir until thickened. Season with salt and pepper.
Flake fish into baking dish, alternating layers with sauce. Sprinkle top with shredded cheese.
Bake in preheated oven for 20 to 25 minutes, or until cheese is browned.
