Abstract: A marine filamentous, mat-forming cyanobacteria, which was originally isolated from Zhoushan coastal area in 1985, and kept in the Key Laboratory of Marine Biotechnology, Ningbo University, has exhibited potential application in water cleaning. In order to culture a marine cyanophyte Phormidium sp. in fresh water, three modes of desalination were carried out (mode 1, the alga was directly cultured into fresh water, and followed by change of 2/3 volume of culture medium every 3 days; mode 2,the alga was cultured in 16‰ sea water, and desalinated to be 8‰ in the second day, and total fresh water in the third, and followed by change of 2/3 volume of culture medium every 3 days; mode 3, the desalination process was the same as mode 2, except not followed by the change of culture medium). The growth curve experiment showed that the worst growth condition occurred in mode 3 with negative growth and bleaching phenomena. The changes of fatty acids upon the desalination stress were determined using GC-MS. Total lipids were extracted using Bligh-Dyer method, and free fatty acid and bound fatty acids were separated using silica gel chromatography. After saponification and methylation, the fatty acids were subjected to Shimadzu QP2010 gas chromatography mass spectrometer using AOC-20 autosampler, with SPB-50 column (30m×0.25mm×0.25μm). The fatty acid was qualified by retention time and mass spectrometry, and quantified using relative composition with C19∶0 as internal standard. The results indicated that free fatty acids and bound fatty acids change in different patterns. At first 3 days, the bound fatty acids decrease while free fatty acids increase. Then, after the alga begins to accommodate the environmental conditions, the contents of bound fatty acids are stabilized, and the free fatty acids decrease.When the alga enters into senescent stage, the free fatty acids increase rapidly again. Among each individual fatty acid, the change pattern of free fatty acid C18∶2(n-6) is weird, that it increases all the time during the culture period until the death of the alga, especially in the culture mode 3 (no change of culture medium). Therefore, C18∶2 (n-6) is considered as the growth auto-inhibition compound. Based on the research data, it is proposed that frequent culture medium change and prolonged desalination process could alleviate the unwanted effects of radical changes of fatty acids content.