Lipids were extracted from marine rotifer, Brachionus rotundiformis in order to examine the functionality of lipid enzymatic modification. The fatty acids, palmitic, linoleic, oleic and stearic acids were the dominant forms accounting for approximately 35.8%, 21.5%, 15.9% and 7.7% of the total lipid content, respectively. Lipid fractions were categorized as neutral lipids (38.5%), glycolipids (45.9%) and phospholipids (17.6%), and after extraction from the rotifer were isolated by thin-layer chromatography (TLC) as free fatty acids (FFA), monoacylglycerol (MAG), diacylglycerol (DAG) and triacylglycerol (TAG). The production of polyunsaturated fatty acid (PUFA) concentrate from rotifer lipids was studied using lipase-catalyzed hydrolysis. In addition, rotifer lipids were modified by hydrolysis using lipases such as porcine pancreas, Candida rugosa and Rhizomucor miehei. The lipase from Rhizomucor miehei was effective in extracting linoleic acid (C 18:2), while the lipase from Candida rugosa was effective in palmitic acid (C16:0) extraction.