A novel antimicrobial peptide was isolated and partially characterized from the homogenate of an Asian marine clamworm, Perinereis aibuhitensis Grube. This novel peptide, named Perinerin, was purified to homogeneity by heparin-affinity column and reverse-phase HPLC, and biologically tested with a MTS-PMS colorimetric assay. Perinerin consists of 51 amino acid residues and structurally appears to be highly basic and hydrophobic. It shows marked activity in vitro against both Gram-negative and Gram-positive bacteria and fungi, which indicates a bactericidal effect as well. Perinerin appears to be constitutively present and its sequence is novel among all other known antimicrobial peptides. These results suggest that Perinerin has the potential to serve as a convenient "evaluation marker" for studying alterations in the biochemistry of the host, particularly with respect to environmental changes. In addition, the MTS-PMS colorimetric assay examination of antimicrobial activity appears to be superior to existing methods and may offer more general application in the search for new antibiotic molecules.