Disclosed is linoleic acid isomerases and their application in production of conjugated linoleic acid, which belongs to the technical fields of protein engineering and microbial engineering. The linoleic acid isomerase derived from Bifidobacterium is used to produce the conjugated linoleic acid. The recombinant E. coli containing the linoleic acid isomerase of the invention is added into a reaction system containing linoleic acid and react for 3 h to produce conjugated linoleic acids. The conversion rate of the conjugated linoleic acid of the invented method ranges from 12.1% to 42.1%, and the percentage of cis9, trans11-CLA in the conjugated linoleic acid can reach 84.3% to 89.1%. The invention provides a method for using microorganisms to produce conjugated linoleic acids with high safety and yield where cis9, trans11-CLA isomer is the major form in the conjugated linoleic acid products.