The aim of this work was to study the seasonal variations of the proximate compositions, fatty acids contents, and related lipid indices (atherogenic index [AI], thrombogenic index [TI], and polyene index [PI]) of golden grey mullet (Liza aurata) and gold band goatfish (Upeneus moluccensis) caught from the northeastern Mediterranean Sea. Proximate compositions and fatty acid contents of both fish species showed statistically significant seasonal variations (p<0.05). The lipid contents were highest in autumn and lowest in winter in golden grey mullet and gold band goatfish. The main saturated and unsaturated fatty acids were palmitic acid (C16:0), stearic acid (C18:0), palmiteoleic acid (C16:1n-7), oleic acid (18:1n-9c), arachidonic acid (C20:4n-6), eicosapentaenoic acid (EPA, C20:5n-3), and docosahexaenoic acid (DHA, C22:6n-3). The total polyunsaturated fatty acids in gold band goatfish did not show any differences among the seasons, whereas that in golden grey mullet was highest in winter. Levels of EPA, DHA, and n-3/n-6 ratios, as well as AI, TI, and PI, were significantly changed among seasons. The results show that golden grey mullet and gold band goatfish, which are among the important fish in Turkey and of commercial value, are a good source for human consumption in terms of their nutritional quality.