PROBLEM TO BE SOLVED: To provide a new enzyme that substrate-specifically hydrolyses specific glycerol-3-phosphodiester and a method for preparing it.SOLUTION: Provided is an enzyme having a substrate-specific hydrolysis activity to glycerol-3-phosphodiester and including a polypeptide described in one of the following (a) - (c): (a) a polypeptide having a specified amino acid sequence; (b) a polypeptide having substitution, insertion, deletion and/or addition of one more amino acids in the amino acid sequence of (a), and having the hydrolysis activity; and (c) a polypeptide having at least 80% homology to the above amino acid sequences and having the hydrolysis activity. Provided is a novel enzyme (GPE-EP) having a high enzyme activity specifically onto glycerol-3-phosphoethanolamine (GPE).