In today’s scenario, algae are widely recognized as a promising source for biofuel production as a renewable source of energy. They are exceedingly rich in oil, which can be converted to biofuel. This paper deals with one of the method to enhance the lipid content in microalgae. The macroalgae Padina boergesenii was collected from Rameswaram, Dist. Tamil Nadu, India and Chlorella vulgaris was collected from Presidency College (Autonomous), Chennai, Tamil Nadu, India. Chlorophyll a, Chlorophyll b and β Carotene were extracted from the selected macro and microalgae which showed the variation among both the species. High amount of lipid was extracted from Chlorella vulgaris when compared to Padina boergesenii. These lipids were analyzed for Transesterification and determined the Omega -3 Fatty acids by GC-MS and FT –IR analysis from the selected Macro and Micro algae.