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Oysters are widely distributed worldwide, but are mainly concentrated in tropics and subtropics. Total lipid (TL), fatty acid (FA) composition of TL and polar lipid (PoL) fractions, phospholipid (PL) class, and molecular species composition in soft tissues of Crassostrea lugubris were investigated for the first time from Vietnam. Phosphatidylglycolic acid (PGA) is the new phospholipid class first identified in marine species in general and Crassostrea lugubris in particular. Main eight classes of PL were determined in PoL fraction: diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylserine (PS), ceramide aminoethylphosphonate (CAEP), CAEP with hydroxylated FAs (CAEP‐OH), and lysophosphatidylcholine. PE and PC accounted for approximately 63% of total known PL. Polyunsaturated FAs accounted for more than 30% of TL. Ninety molecular species of glycerophospholipids, including PGA, PE, PC, PS, PI, DPG, and PG, and sphingophosphonolipids (CAEP) were identified in PoL. Alkenyl‐acyl forms of glycerophospholipids were predominated in the molecular species of PGA, PE, and PS. PGA 38:1 (p18:0/20:1), PE 40:6 (p18:0/22:6 and p18:1/22:5), PC 30:0 (14:0/16:0), PS 38:1 (p18:0/20:1), PI 40:5 (20:1/20:4), PG 32:0 (16:0/16:0), DPG 88:24 (22:6/22:6/22:6/22:6), and CAEP 34:2 (d18:2/16:0) were major molecular species. [ABSTRACT FROM AUTHOR]