Abstract: GC-MS and HPLC were applied to determine the flavor substance and fatty acid of Carassius auratus in Long Lake and Carassius auratus gibelio and to identify the relevant difference between them. The results indicated that there was no obvious difference between the hexanal contents in the muscles of both fresh Carassius auratus in Long Lake and Carassius auratus gibelio,and the hexanal contents in both fish could be respectively increased by 9.72 times and 43.17 times through heating. EPA and DPA in fatty acid of fresh Carassius auratus in Long Lake respectively were 2.76±1.28 and 9.35±1.17,which were much higher than that of Carassius auratus gibelio(EPA 0.98±0.24 and DHA 3.71±0.71),and this difference was much more obvious after heating. The inosinic acid(IMP) content of fresh Carassius auratus in Long Lake was lower than that of fresh Carassius auratus gibelio,however,after heating,the inosinic acid(IMP) content of Carassius auratus gibelio was slightly decreased,on the contrary,the inosinic acid(IMP) content of Carassius auratus in Long Lake was sharply increased with the absolute content higher than that of Carassius auratus gibelio under the same treating condition. Small peptide in the two kinds of fish was rich with peptide 2 as the primary component. The peptide 2 content in Carassius auratus gibelio was obviously higher than that of Carassius auratus in Long Lake( p < 0. 05), after heating, the peptide contents in both kinds of fish were significantly decreased,but there was still significant difference(p<0.05) between them.