Effects on the fatty acid composition of cod (Gadus morhua) and salmon fillets (Salmo salar) after pan-frying in margarine and olive oil were determined. The fatty acids of the margarine used were 55.5% saturated (SFA), 33.0% mono-unsaturated (MUFA) and 11.5% polyunsaturated (PUFA). The olive oil used contained 15.4% SFA, 76.1% MUFA and 8.5% PUFA. Using margarine or olive oil increased the SFA and MUFA percentages, respectively, in both species. For cod fillets (lean), pan-frying increased the fat content (0.55–4.15g/100g and 0.55–2.30g/100g before and after pan-frying, with margarine and olive oil, respectively), whereas, for salmon fillets (fat), it decreased (13.91 to 10.57g/100g and 15.35 to 12.95g/100g before and after pan-frying with margarine and olive oil, respectively). In conclusion, the culinary fat selection affects the total fatty acid content and composition of the prepared fish fillet.