This study was designed to examine the effect of thermal acclimation on the lipid composition of fat depot organs the liver and kidneys of larval sea lamprey, Petromyzon marinus. We found that 21°C-acclimated larvae possessed lower total lipid amounts in the liver (39% lower) and kidneys (30% lower) than 13°C-acclimated larvae. Relatively lower lipid contents in the liver and kidneys of 21°C-acclimated lamprey primarily resulted from a reduction in stored lipid reserve, triacylglycerol, but not the structural lipid, phospholipid. Compared to 21°C-acclimated larvae, 13°C-acclimated larvae were found to possess fewer saturated fatty acids (SFAs) and more unsaturated fatty acids (USFAs) in renal triacylglycerol and phospholipid classes, while there were no significant differences in the SFAs and USFAs of hepatic triacylglycerol, phospholipid, cholesteryl ester, fatty acid, and monoacylglycerol classes. Fewer SFAs, found in the kidney triacylglycerol of 13°C-acclimated lamprey, were due to lower 12:0 and 14:0 fatty acids, but those in the renal phospholipid class were characterized by fewer 14:0, 15:0, and 16:0 fatty acids. More USFAs in renal triacylglycerol, as indicated by a higher unsaturation index, primarily resulted from higher polyunsaturated fatty acids (18:2ω;6, 18:3ω;3, and 18:4ω;3); whereas, in the renal phospholipid class, this was a result of higher monoenes (18:1, 20:1, and 22:1ω;9) and ω;3 polyunsaturated fatty acids (18:4ω;3). These data suggest that the influence of thermal acclimation on the lipid composition of lamprey fat depot organs depends on tissue and lipid class.