Introduction: Arachidonic acid is an important essential fatty acid in human nutrition. The filamentous fungus Mortierella alpina has been identified as a promising producer of arachidonic acid. Mortierella alpine can accumulate up to 40% (w/w) lipid, of which up to 40% can be arachidonic acid. Materials and methods: Mortierella alpina CBS 754.68 was cultivated in low cost substrate such as glucose syrup, brown sugar and starch for lipid and arachidonic acid production. The reduced sugar, total lipids and content of ARA were determined by dinitrosalicylic acid method, soxhlet and Gas chromatography–mass spectrometry (GC-MS) respectively. Results: The carbon sources were applied at 70 g/l and nitrogen source (soybean powder) at 10 g/lit. The results showed that lipid in dry biomass in glucose syrup, starch and brown sugar media were obtained 32, 25 and 13 % w/w respectively. The arachidonic acid contents of lipid in the glucose syrup, starch and brown sugar media were 41, 33 and 31 % w/w respectively. Discussion and conclusion: Lipid fatty acid compositions are affected by the growth of microorganism. Cell membrane fatty acids such as stearic acid and oleic acid increased substantially concomitant with increases in the amount of biomass. Biomass and oil production efficiency fell due to inappropriate brown sugar medium.