A method for producing cis-5-hydroxy-L-pipecolic acid is described. A gene recombinant microorganism enabling direct production of cis-5-hydroxy-L-pipecolic acid can be used in the method. Also described is a gene recombinant microorganism. In particular, it is described that a gene recombinant microorganism having DNAs encoding proteins involved in the biosynthesis of L-pipecolic acid and a DNA encoding a protein having the L-pipecolic acid cis-5-hydroxylase activity is cultured in a medium, and cis-5-hydroxy-L-pipecolic acid is collected from the medium.