Abstract: The fatty acid composition of five species of microalgae and the effect of domestication with seawater and freshwater on them were studied. The results suggest that each class of microalgae is characterized by a specific fatty acid profile. The specific features of freshwater alga Chlorella Pyrenoidosa, marine algae Chlorella sp.-1 and Chlorella sp.-2 are high content of 16:0, 16:2, 18:0, 18:2 and 18:3; The freshwater alga Scenedesmus obliquus is characterized by high content of 16:0, 18:1 and 18:3; The reliable marks of the marine diatom Phaeodactylum tricornutum are rich in 14:0, 16:0, 16:1, 16:2, 18:0 and 20:5, especially in 16:0 and EPA. Alter domestication, the kind of "characteristic" fatty acids was not changed, but the content of the main fatty acids changed. The content(mg/g cell dry wt)of "characteristic" fatty acids and total fatty acid in C. pyrenoidosa, Chlorella sp.-1 and the clone SS02 of P. tricornutum increased to a certain degree, while the results were opposite in S. obliquus, Chlorella sp.-2 and the clones ZS08, XS03 of P. tricornutum.