Michelia champaca and Garcinia indica seeds yielded 45.0% and 45.5% of oil. The fatty acid profiles of both the seed oils were examined. The saponification value (SV), iodine value (IV) and cetane number (CN) of fatty acid methyl esters of both the seed oils were empirically determined. The saponification value (SV) and iodine value (IV) are in good agreement with the experimentally observed values. The fatty acid compositions, iodine value and cetane number were used to predict the quality of fatty acid methyl esters of oil for use as biodiesel. Thus, the fatty acid methyl esters of seed oils of M. champaca and G. indica were found to be the most suitable biodiesel and they meet the major specification of biodiesel standards. The selected plants M. champaca and G. indica have great potential for biodiesel. M. champaca and G. indica seed oils were found to contain keto fatty acids along with the other normal fatty acids, respectively. These fatty acids have been detected and characterized by UV, FTIR, H-1 NMR, C-13 NMR, MS, GC techniques and chemical transformations. (C) 2008 Elsevier Ltd. All rights reserved.