It is known that the unsaturated fatty acids in natural fats and oils are generally produced in cis-form. However, these acids change from cis to trans-form by physical or chemical treatments, -heat, light and various catalysts. The purpose is to study the origin and mechanism of these isomerizations.The fatty acid methyl ester of linseed oil was used as sample. The separation methods of the unsaturated fatty acid in this study were urea complex method, bromination-debromination method, hydroxamic acid method and low temperature crystallization. The isomerization degree of these esters by the above methods were compared.The result was as follows; 1) Urea complex method : Methyl linolenate was concentrated up to 69% by this method, but the efficiencey of separation was not high. More than 2% of conjugated diene was yielded, it was found to be cis-trans conjugated isomer.2) Fromination-debromination method : This is an effective method for separating the methyl linolenate of high purity, estimating from iodine value. The yeild was about 22%. Even by the careful treatment, it gave about 0.6% conjugated diene which was found to be trans-trans conjugated isomer. It was also found that the trans non-conjugated isomer was formed by this method.3) Hydroxamic acid method : Methyl linolenate of high purity was obtained in 26% yield by this method. Formation of conjugated isomer was not observed, but little amount of the trans non-conjugated isomer was detected.4) Low temperature crystallization method : Although the yield of pure material was only 8.4%, this method was found to be the best, since any isomer was not formed by this treatment.Then, the most practical method will be the combination of this method with urea complex method.