The pure microalgal species such as Anabaena sp., Nostoc sp., and Phormidium sp., were collected and isolated from marakkanam salt pan (water samples), tamilnadu. The culture was harvested in BG11, microalgae can be used to produce energy in different process; it is one of the best effective methods, to convert the algal oil derivatives in to biodiesel. These selected potential microalgal species were subjected to fatty acids extraction and transesterification to determine the fatty acid compounds by GC-MS and FT-IR analysis for the production of biodiesel. The Palmitic acids, Pentadecanoic acid, Oleic acid, Octadecanoic acid, Eicosedenoic acid etc., were accumulated from the selected micro algal species. The FT-IR spectrum retrieved from the FAME of all the three microalgal strains strongly confirms the presence of hydroxyl group, alkenes group, alkanes group, alkynes group, esters and aromatic groups.