To understand the mechanism of lipid accumulation and the corresponding metabolic changes of the microalga Nannochloropsis oceanica IMET1, the lipid content, fatty acid composition and metabolic profile were investigated via batch culture under nutrient deficiency and chemostatic culture under nitrate limitation. The results indicated that the triacylglycerol-neutral lipids were significantly accumulated through an acyl-CoA dependent pathway, while the polar lipids were partially converted to triacylglycerol through an acyl-CoA independent pathway. The fatty acid compositions of the polar lipids changed concurrently with the length of time of the nutrient deficiency, while the fatty acid compositions of the neutral lipids remained nearly consistent. The concentrations of several major osmolytes were significantly changed under chemostatic conditions with different nitrogen concentrations, which reflect the membrane property changes caused by the alteration of the polar lipid composition. (C) 2012 Elsevier Ltd. All rights reserved.