The lipid and fatty acids of the Pacific oyster, Crassostrea gigas, collected both in Japan and France, were analyzed. Triacylglycerols and sterols were the major classes in the neutral lipids of both populations of C. gigas between the two countries, and they had significant levels of phospholipids (phosphatidylethanolamine and phosphatidylcholine) with ceramideaminoethylphosphonate in their polar tissue lipids. The differences of 18:3n-3 and 22:6n-3 (docosahexaenoic acid; DHA) levels in the depot triacylglycerols suggest the influence of dietary phytoplankton in different environments of the two countries. Although the levels of the fatty acids slightly differed, that of 20:5n-3 (icosapentaenoic acid; EPA, 20.5-24.8%) in the triacylglycerols was specifically the highest fatty acid in all the samples. The major polyunsaturated fatty acids in the polar lipids of all samples were EPA (13.2-17.8% for phosphatidylethanolamine and 13.4-22.7% for phosphatidylcholine) and DHA (18.9-26.8% for phosphatidylethanolamine and 13.1-22.5% for phosphatidylcholine). The fluctuation of total PUFA levels in the polar lipids between samples of both countries suggests the influence of diet. In addition, the consistently high EPA levels in the phospholipids may compensate for the variation in DHA levels.