This study was designed to evaluate biochemical changes in the fatty acid (FA) compositions of selected lipid depot (kidney and liver) and absorption (intestine) organs in larvae and metamorphosing sea lamprey, Petromyzon marinus. Palmitic or stearic acids were generally the predominant saturated fatty acids (SFA) before and during metamorphosis, but the greatest proportion of myristic acid occurred in renal triacylglycerol (TG). Monoenes, dienes, and polyenes consist mainly of 16:1, 18:1, and 20:1, 18:2 and 20:2ω6, and 18:4ω3, respectively. Alterations in these predominant fatty acids occurred during lamprey metamorphosis, but depended on tissue, lipid class, and developmental status. During metamorphosis, kidney TG and phospholipid (PL) classes tended to mobilize SFA and enhance the fatty acid unsaturation, as indicated by increased unsaturated/saturated ratio, unsaturation index (USI), and total mean chain length (MCL). There was a tendency to increase saturation in the fatty acids of liver TG and PL classes and intestine TG, FA and monoacylglycerol (MG) classes, but to increase unsaturation in the fatty acids of liver cholesteryl ester (CE), FA and MG classes and intestine PL and CE classes from larva or stage 3 to stage 7. Increased polyunsaturated fatty acids in kidney TG and PL from larvae to stage 5 transformers and intestine PL and CE from stage 3 to stage 7 transformers may reflect an osmoregulatory pre-adaptation. The presence of branched-chain SFA (BCSFA) and the odd number of fatty acids (ONFA) indicated a significant role of detritivores in the benthic larvae. Decreased abundance of BCSFA, ONFA, and 18:2 dienes occurred in the transformed intestine TG as non-trophic metamorphosis proceeded. These data suggest that sea lamprey metamorphosis may proceed in a habitat, dietary, osmoregulatory, energetic, and developmental pre-adaptation of fatty acid composition from benthic filter-feeding larvae to pelagic parasitic juveniles.