A malonyl-CoA-independent fatty acid synthetic system, different from the systems in other subcellular fractions, occurred in mitochondria of Euglena gracilis. The system had ability to synthesize fatty acids directly from acetylCoA as both primer and C , donor using NADH as an electron donor. Fatty acids were synthesized by reversal of fi-oxidation with the exception that enoyl-CoA reductase functioned instead of acyl-CoA dehydrogenase in degradation system. A fairly high activity of enoyl-CoA reductase was found on various enoyl-CoA substrates (C, -C,,) with NADH or NADPH. Three species of enoyl-CoA reductase, distinct from each other by their chain-length specificity, were found in Euglena mitochondria, and one of them was highly specific for crotonyl-CoA. It is also discussed that the mitochondrial fatty-acid synthetic system contributes to wax ester fermentation, the anaerobic energy-generating system found in the organism.We have reported in the preceding paper [I] that when aerobically grown Euglena gracilis is placcd under anaerobic conditions, paramylon, the reserve poly5accharide, is promptly converted into wax esters with concomitant generation of ATP, and this phenomenon has been named as the wax ester fermentation. In Euglena occurrence of four systems of fatty acid synthesis has been reported [2], namely, one involving multifunctional fatty acid synthetase in cytosol [3 -71, two acyl-carrier-protein-dependent systems in chloroplasts (one being a chain-elongation system) [4-6 , 8 -101 and one involving a fatty acid synthetase in microsomes [II, 121. In the wax ester fermentation, thesc known systems of fatty acid synthesis cannot explain the net gain of ATP, since consumption of ATP by formation of malonyl-CoA and transfer of acetyl unit from mitochondria to other subcellular sites exceeds generation of ATP in glycolysis. Existence of an unknown system of fatty acid synthesis which explain the net gain of ATP in wax ester fermentation is accordingly suggested.In the present paper we report that a malonyl-CoA independent fatty acid-synthetic system occurs in mitochondria of E. gracilis and that the system has ability to synthesize fatty acids directly from acetyl-CoA as both primer and C, donor unlike other malonyl-CoA independent systems of fatty acid synthesis in mammalian mitochondria [I 3 -161, chloroplasts of spinach [17] and Mycohacterium smegmutis [18, 191. It is also discussed that the mitochondrial system of fatty acid synthesis contributes to the wax ester fermentation.