The lipid and FA composition of the total lipids of the pearl oyster Pinctada fucata martensii, in different seasons and in different areas, were analyzed to clarify its lipid physiology and to estimate the possible influence of its prey phytoplankton. During the spawning season (June and July), the lipid contents were slightly higher than in the growing season (November and March). TAG and sterols were the major components in the neutral lipids in all conditions, whereas high levels of phospholipids (PE and PC) were found in the polar lipids. In addition, significant levels of ceramide aminoethyl phosphonate but low levels of sphingolipids were found in the polar lipids. The major FA in the TAG in all samples were 14:0, 16:0, and 18:0 as saturated FA (saturates); 16:1 n-7, 18:1 n-9, and 18:1 n-7 as monoenoic FA (monoenes); and 20:4n-6 (arachidonic acid: AA), 20:5n-3 (EPA), and 22:6n-3 (DHA) as PUFA. The major components found in the polar lipids were 16:0 and 18:0 as saturates; 22:2n-9,15 and 22:2n-7,15 as non-methylene-interrupted dienes (NMID), and AA, 22:3n-6,9,15, EPA, and DHA as PUFA. Similar to the high levels of total PUFA in the phospholipids, comparatively high PUFA levels were found in TAG in both the growing and the spawning season. This may be a characteristic of the species as a typical bivalve, because the lipids were similar to those of other bivalves. Although it is a marine animal, uncharacteristically high levels of AA were found in both the TAG and phospholipids. This result suggests that lipids of P. fucata may be influenced by those of its phytoplanktonic prey. The increase in levels of NMID from TAG to PE with a decrease in those of monoenes suggests that the tissues of this species are able to biosynthesize only the less unsaturated PUFA, such as NMID. In particular, NMID derivatives are considered to be biosynthesized in the PE; thus, they might play a particular role in the membrane, because NMID were characteristically localized only in the PE.