The quality and quantity of food organisms in fish seed production are important. The marine microalgae Nannochloropsis oculata are used as initial food organisms in the field. We investigated the effects of salinity (0, 10, 20, 30, 40 and 50 psu) on the lipid and fatty acid composition of N. oculata. Cultivation of N. oculata at varying salinities showed the highest growth rate at 20 psu. Total lipid content ranged from 17.26 to 18.63% at salinities from 0 to 50 psu). The nonpolar lipid content increased markedly at 30 psu and was highest at 15.55%. The polar lipid content was lowest at 30 psu, by 84.45%. It was also found that the omega-3 and EPA contents were inversely proportional to salt concentration. For the polar and nonpolar lipid compositions, there was no significant effect of salinity. Omega-3 polyunsaturated fatty acid content especially the content of EPA in the seawater larvae is the essential fatty acid in this food organism. It is thus advantageous to culture N. oculata at 20 psu.