Spiny icefish (Chaenodraco wilsoni) is an important species of crocodile icefish native to the high-Antarctic of the Southern Ocean, including the Bransfield Strait. The water mass in the Strait is complex, with warm, low-salinity surface waters found in the western and northern BS and colder, more saline waters of the Weddell Sea over the broad continental shelf near d′Urville and Joinville Islands. The local food availability of C. wilsoni may be influenced by those waters. The fatty acids can considered as dietary tracers to explore feeding habits of fish sepcies. So the present study examine the fatty acids composition of C. wilsoni and further explore the effect of waters on local food availability of C. wilsoni. The results demonstrate twenty-seven kinds of fatty acids are detected from the muscle of C. wilsoni, which consist of eleven kinds of saturated fatty acids (SFAs), eight monounsaturated fatty acids (MUFAs), and eight polyunsaturated fatty acids (PUFAs). The significant difference in marker fatty acids of C. wilsoni between the Transitional Zonal Water with Bellingshausen Sea influence (TBW) and the Transitional Zonal Water with Weddell Sea influence (TWW) in the Bransfield Strait. C. wilsoni presents more omnivorous feeding for the TBW region, but more carnivorous feeding for the TWW region.