Small pelagic fishes such as sardine and anchovy are among the richest species in essential fatty acids that are eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), whose bioavailability may depend on its esterification to polar or neutral lipids. The EPA and DHA quantities in neutral and polar lipids were compared in sardine (from the English Channel) and anchovy (from the Bay of Biscay) fillets, and in red and white muscle separately. Sardine fillets had the highest EPA+DHA content (760 ± 670 vs 370 ± 510 mg/100 g in anchovy fillets), mainly because of their largest proportion of lipid-rich red muscle and its relatively high lipid content. However, DHA esterified to polar lipids was higher in anchovy than in sardine fillet (270 ± 60 vs 230 ± 30 mg/100 g). EPA+DHA content were higher in red than white muscle for both species. This study highlights the nutritional interest of red muscle to provide essential dietary fatty acids to consumers, and the necessity to consider its importance in nutrition studies.