The biology of Aurantiochytrium sp. KRS101 was thoroughly investigated to enhance its production of biodiesel and docosahexaenoic acid (DHA). Nutrients and salinity were optimized to prevent biomass loss due to cell rupture. Calculation of yield coefficients showed that nitrogen was mostly responsible for the early stage of cell growth or division, whereas carbon was necessary for the entire process of cell development, particularly cell enlargement during late stages. Using these distinctive yield coefficients, a modified fed-batch cultivation method was designed, resulting in increases in palmitic acid (PA) and DHA production of up to 137% and 29%, respectively. This modified fed-batch cultivation method, using appropriate supplies of nitrogen and carbon, may improve the yields of PA and DHA, thus expanding the biotechnological applications of Aurantiochytrium sp. KRS101. (C) 2012 Elsevier Ltd. All rights reserved.