Depletion of petroleum based fuel turns the world’s focus in to finding a new alternative in which biodiesel took major attention. Biodiesel is produced from various sources like waste vegetable oil, animal fat, grease etc. In this, macro algae Cladophora vagabunda was studied with different solvent systems such as isopropanol and chloroform-methanol for better yield of biodiesel. Among these solvent system, chloform-methanol solvent system produced more biodiesel(3.3ml/10gm) than isopropanol solvent system (2.6ml/10gm). Since Cladophora vagabunda with chloform-methanol solvent system produced more biodiesel its esters of fatty acid content was analyzed by using Gas chromatography coupled with mass spectrometer. The results showed that the presence of ethyl palmitate as the dominant ester with percentage composition of 9.36% than methyl palmitate 9.18%. But the overall percentage of methyl ester compound was found to be more (21.66%) than ethyl ester (14.97%). The major fatty acid compounds were also analyzed. These include myristic acid (1.93%), linolenic acid (0.60%) and palmitic acid (9.18%).