Microalgae biodiesel can be a suitable alternative for fossil fuel in future. They are considered as better third generation biodiesel feed stock and can adapt in wide variety of environ-ment and adverse environment such as domestic and industrial effluents. Hence selection of oleagi-nous microalgae based on native biomass and lipid production is an important step. In this study Chlorella sp designated as MS3 isolate was isolated from fresh water and its lipid content was analysed through Fourier transform infrared (FT-IR) spectroscopy. FT-IR spectra of MS3 isolate con-sist of higher percentage of fatty acids including oleic, palmetic, linolenic acid. As a result, FT-IR based lipid analysis of MS3 isolate can be selected as oleaginous microalgae for further biodiesel feed stock preparation.