Seasonal variation on fatty acid composition of 51 algal species from Gulf of Mannar Marine Biosphere Reserve has been studied. Analysis of fatty acids by gas chromatography revealed the presence of higher amount of saturated fatty acids than unsaturated fatty acids. Among the saturated fatty acids, the amount of palmitic acid was higher (96.88%) in all the seasons and species studied. In the present investigation, the highest relative percentage of lauric acid (31.58%), tridecanic acid (4.46%), nonadecanoic acid (2.06%), heneicosanoic acid (23.9%), oleic acid (21.38%) and linolenic acid (10.42%) were recorded during spring season from Ulva lactuca, Acanthophora spicifera, Valoniopsis pachynema, Turbinaria decurrens, Stoechospermum marginatum and Cheilosporum spectabile respectively. Highest percentage of heptadecanoic acid (12.36%) and behenic acid (8.92%) were recorded during monsoon season from Caulerpa taxifolia and Terbinaria ornate. Myristic acid (24.71%), pentadecanoic acid (3.29%), palmitic acid (96.88%), stearic acid (6.99%) and linoleic acid (28.61%) were high in Halimeda tuna, Valoniopsis pachynema, Ulva fasciata, Bryopsis plumose and Ulva reticulata respectively during post monsoon season. Padina tetrastromatica showed the highest relative percentage of arachidic acid (12.6%) during summer.