The present invention provides a method for producing Nε-dodecanoyl-L-lysine using an enzyme having properties suitable for the industrial production of Nε-dodecanoyl-L-lysine. More specifically, the present invention provides a method for producing Nε-acyl-L-lysine including reacting a carboxylic acid or a salt thereof and L-lysine or a salt thereof in the presence of a protein having an amino acid sequence of SEQ ID NO: 1; a protein having an amino acid sequence in which one or several amino acid residues are inserted, added, deleted, or substituted in the amino acid sequence of SEQ ID NO: 1 and having Nε-acyl-L-lysine-specific aminoacylase activity; and a protein which has 90% or higher homology with the amino acid sequence of SEQ ID NO: 1 and having Nε-acyl-L-lysine-specific aminoacylase activity.