Lipid class composition and distribution of fatty acids within the lipid pool of microalga, Schizochytrium mangrovei FB3 harvested at the late exponential phase, was studied, with special emphasis on the distribution of docosahexaenoic acid (C22:6 n-3, DHA). Neutral lipids were the major lipid constituents (95.90% of total lipids) in which triacylglyerol (TAG) was the predominant component and accounted for 97.20% of the neutral lipids. Phosphatidylcholine (PC) was the major polar lipid. Phosphatic acid and phosphatidylserine were the two classes in phospholipids reported for the first time in thraustochytrids. Both TAG and PC were primarily saturated and consisted of C16:0 at approximately 50% of total fatty acids. DHA was found to be distributed in all lipid classes and to be the major polyunsaturated fatty acid. TAG contained the highest amount of DHA, although the percentage of DHA in total fatty acids in TAG (29.74%) was lower than that in PC (39.61%). The result from this study would be useful for further optimization of DHA production by S. mangrovei.