The aim of this work was to describe and compare the main fatty acids and biodiesel indices of some green and brown macroalgae (seaweeds) collected from the Persian Gulf, as an alternative raw material for renewable biodiesel production. The macroalgae showed low lipid content (< 10% DW) but marine macroalgae with total lipid content > 5% DW are a good source for biodiesel production. The total lipid content and saturated fatty acids (SFAs) of green algae were higher than that of brown algae, while higher accumulation of unsaturated fatty acids (USFAs) was observed in brown seaweeds. Further, the main fatty acid in all studied seaweeds was palmitic acid (C16:0), which was followed by oleic acid (C18:1). The results of this work showed that three of the green algae, especially C. sertularioides, could be a potential source of fatty acids for biodiesel production owing to their high total lipid content, high cold flow indices (long chain saturated factor, cold filter plugging point and cloud point) and a fatty acid profile rich in SFAs with a high amount of C18:1, which is suitable for oil-based bio products. In contrast, the brown seaweeds Sargassum boveanum and Sirophysalis trinodis lipid content had a high proportion of polyunsaturated fatty acids (PUFAs), which makes them suitable for replacing fish oil.