In order to gain fundamental information on the utilization of lipids as energy source in mud-skipper, muscle lipids and their fatty acid composition were investigated with respect to life cycle-maturation (Aug), before-hibernation (Nov), and after-hibernation (Apr). Crude and neutral lipid were found to decrease from 1.2, 68.3% (Aug) via 0.7, 53.8% (Nov) to 0.4, 42.6% (Apr), respectively, whilst phospholipids and glycolipids increased from 29.5 and 2.2% (Aug) to 52.1 and 5.3% (Apr), respectively. In neutral lipids, TG contents gradually decreased from 53.8% (Aug) via 33.6% (Nov) to 23.1% (Apr), while FFA and sterol contents increased from 13.5 and 14.2% (Aug) to 22.3 and 24.5% (Apr), respectively. In phospholipids, PC content decreased from 61.2% (Aug) to 50.6% (Apr), while changes in PS and PE contents, as a whole, showed the opposite trends. In neutral lipids, the levels of some fatty acids such as 16:0, 16:1, 18:0, 18:1 and 20:5 (ω3) were analyzed to be high, with the 20 : 5 being predominant, and the levels of saturated and monoene-acids gradually decreased, while polyene-acids increased in before and after hibernation. In before hibernation, 16:0, 16:1, 18:1 mainly decreased but 18:2, 18:3 (ω3) and most of saturated and monoene acids such as 14:0, 14:1, 16:1, 18:0, 18:1 slightly decreased in after hibernation. From these findings, it was suggested that those fatty acids decreased during hibernation were used as a energy source, particularly 16:1 and 18:1 being most preferentially used. In phospholipids, the levels of 16:0, 18:0, 20:5 (ω3), 22:5 (ω3) and 22:6 (ω3) were found to be high. Throughout the life cycle, the levels of monoene-acids in phospholipids stayed constant, whilst those of 18:2, 18:3 (ω3) and saturated acids such as 16:0, 18:0 were found to be decreased gradually in before and after hibernation, whereas those for the high degree of polyene-acids such as 20:4 (ω6), 20:5 (ω3), 22:5 (ω3), 22:6 (ω3) increased, particularly 20:4 (ω6), 20:5 (ω3) being most increased.