The single stage process of simultaneous extraction and transesterification result in higher biodiesel yield as compared to extraction followed by transesterification in two stages. The spectra of NMR and FTIR and gas chromatographic analysis data showed very clearly that algae biodiesel obtained from Spirulina and pond water algae biomass were composed of fatty acid methyl esters. Gas chromatographic analysis data also showed that algae biodiesel derived from Spirulina and pond water algae mainly composed of palmitic acid methyl ester. Pond water algae biodiesel has more percentage of oleic and palmitoleic acid methyl ester as compared to Spirulina biodiesel. On the other hand, Spirulina biodiesel has more linoleic and linolenic acid methyl ester as compared to biodiesel derived from pond water algae. Fuel properties of algae biodiesel show that biodiesel from Spirulina algae and pond water algae were comparable in quality with that of other conventional biodiesel. Based on the fatty acid composition and the fuel properties, it is concluded that biodiesel produced from Spirulina and pond water algae could be a good alternate to conventional diesel.