Effects of sodium chloride (NaCl) concentration on the lipid and fatty acid profiles of the polyunsaturated fatty acid (PUFA)-producing fungus, Mortierella alpina SC9, were investigated. The cells were cultivated in the medium with 4 different NaCl concentrations (0, 1, 2, 4%) for 6 days. The lipid and fatty acid profiles were analyzed by thin layer chromatography and gas chromatography. In the cultures with NaCl concentration up to 2%, PUFAs accounted for over 50% of the total fatty acids (TFAs) of the cells. Triacylglycerol (TAG) was the major lipid class, followed by monoacylglycerol (MAG) and diacylglycerol (DAG). TAG was found to contain the highest proportion of arachidonic acid (C20:4n-6, AA), suggesting that AA was mainly stored in the TAG. Comparing cultures at different NaCl concentrations indicated that TFA and TAG contents were higher in the cells grown at 2% NaCl. Similar results were found when 2% NaCl was added at day 3 of cultivation (late-log phase). In addition, the gene expression level of a TAG biosynthesis enzyme, diacylglycerol acyltransferase 2 (DGAT2), was also higher in the NaCl treated cells. This suggested that the increase of TFA and TAG contents might be related to the NaCl-stimulated DGAT2 expression.