Perinerin is a small antimicrobial peptide (AMP) isolated from an Asian marine clamworm, Perinereis aibuhitensis Grube. It shows marked activity in vitro against both Gram-negative and Gram-positive bacteria. To obtain it in large amounts, the coding sequence of perinerin was cloned into pET32a(+) vector and expression as a Trx fusion protein in Escherichia coli. The soluble fusion protein collected from the supernatant of the cell lyste was separated by Ni(2+)-chelating chromatography. The purified protein was then cleaved by Factor Xa protease to release mature perinerin. Final purification was achieved by ion-exchange chromatography. Recombinant perinerin exhibited a similar antimicrobial activity to the native perinerin. These works might provide a significant foundation for the following research on the action of mechanism of marine AMPs.