In the current study, the effect of frozen storage at −18°C was evaluated on fatty acid composition of different body parts (liver, muscle tissue, and viscera) of narrow-barred Spanish mackerel (Scomberomorus commerson, Lacépède, 1800), longtail tuna (Thunnus tonggol, Bleeker, 1851), kawakawa (Euthynnus affinis, Cantor, 1849), king mackerel (Scomberomorus guttatus, Bloch & Schneider, 1801), and rainbow sardine (Dussumieria acuta, Valenciennes, 1847) caught in the Persian Gulf. Changes in saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid plus docosahexaenoic acid/palmitic acid (EPA+DHA/C16), ω3 PUFA/ω6 PUFA (ω3/ω6), and polyunsaturated fatty acids/saturated fatty acids (PUFA/SFA) were investigated during a 6-month period. A decrease in unsaturated fatty acids, particularly PUFAs (60–100%) as well as ω3/ω6, EPA+DHA/C16 (polyene index) and PUFA/SFA ratios, indicated a decrease in the nutritional values of the samples.