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The effect of ambient temperature on the composition of intracellular fatty acids and the release of free fatty acids (FFA) into a medium by cyanobacterium Spirulina platensis and eukaryotic microalgae, Chlorella vulgaris and Botryococcus braunii, was studied using their batch cultures. It was found that all the species studied, regardless of their taxonomic status, responded to the temperature regime by similar changes in their intracellular fatty acid composition: the relative content of more unsaturated fatty acids decreased with the elevation of temperature. At the same time, in the prokaryote, this temperature shift blocked, first of all, the elongation of 16:0 to 18:0 and then their further desaturation. In eukaryotes, the change in the desaturation of dienoic to trienoic fatty acids was the most pronounced process. The ratio of dienoic to trienoic fatty acids remained almost unchanged in S. platensis. The relative content of extracellular unsaturated FFA increased in the prokaryotic organism S. platensis at a higher temperature. But no significant changes in the composition of extracellular unsaturated FFA were detected in eukaryotic algae upon temperature elevation.