Bioenergy is one of the most important components to mitigate greenhouse gas emissions and substitute of fossil fuels. The need of energy is increasing continuously, because of increases in industrialization and population. The basic sources of this energy are petroleum, natural gas, coal, hydro and nuclear. The ability of algae to fix Co2 can also be an interesting method of removing gases from power plants, and thus can be used to reduce greenhouse gases with a higher production algal biomass and consequently higher biodiesel yield. Present research such as biodiesel from macroalgae having species Sargassum ilicifolium and Turbinaria ornata. Biodiesel production (methyl ester) was found maximum in Sargassum ilicifolium (8.01%) and minimum in Turbinaria ornate (7.03%).More over sediment (glycerine, pigments and other elements) were higher in Turbinaria ornate(4.26g) than in Sargassum ilicifolium(2.93g). It was observed that Turbinaria ornata could produce large amount of poly unsaturated fatty acids (PUFA) as the major storage lipid which accounted 80.44% than the Sargassum ilicifolium is about 75.98% respectively. Since intracellular lipids can be enhanced by controlling the conditions such as nutrient limitation, limitation of light and salt stress, it can be expected that the TAG yield of macro algae can further be increased by the same approaches. This may be a First report in India that the biodiesel producing macroalgae, their detailed ultrastructure and the lipid droplets storage. If we go further to demonstrate this model in the coastal India, there will be a larger opportunities to produce cost effective biofuel or biodiesel and glycerine production as well as the rural employment creation.