Dietary preferences of archaeological and paleontological animals have been investigated based on stable carbon isotope ratios (δ<sup>13</sup>C) of collagen and non-collagenous proteins in fossil bones. The δ<sup>13</sup>C of individual compound in lipids from fossil bones were recently applied to the reconstruction of palaeodietary of animals. In the present study, we analyze the concentrations, class distributions, and δ<sup>13</sup>C values of fatty acids and steroids in the Pleistocene to Pliocene fossil whale and the Miocene fossil sea cow (<i>Dusisiren</i> sp.) bones, and evaluate their applicability as indicators of palaeodietary and fossil diagenesis. Biosynthetic steroids as cholesterol are detected in the Pleistocene whale bones, while the sterols are very poor in the older Pliocene whale samples, of which major steroids are their diagenetic compounds such as cholestanes and cholestenes. However, a large amount of cholesterol characterizes the Miocene fossil sea cow bone. We also can identify labile unsaturated fatty acids from all fossil whale and sea cow bones. It is suggested that the relative abundances of unsaturated to saturated fatty acids can be useful indicator for estimating diagenetic stage of fossil bones and checking contamination. The δ<sup>13</sup>C values of fatty acids in the fossil whale and sea cow bones range widely from -25.7 to -16‰, and there are differences of 1 to 4‰ between several fatty acid homologues within the same sample. Thus, the δ<sup>13</sup>C analyses of fatty acids in fossil bones may be less applicable for reconstructing palaeodietary. On the other hand, the δ<sup>13</sup>C values of steroidal compounds within the same sample are almost similar, although these values vary ranging between -29.6‰ and -24.4‰ among the different whale samples. Furthermore, the steroidal δ<sup>13</sup>C value in the sea cow sample is -20.5‰, which is concordant with that of food in sea cow. From these results, the δ<sup>13</sup>C value of steroid in fossil bone can be strongly useful tool for reconstructing palaeodietary of paleontological animal.