<jats:p>A novel antimicrobial peptide, named misgurin, was isolated and characterized from the loach (mudfish), <jats:italic>Misgurnus anguillicaudatus</jats:italic>. The 21‐amino‐acid peptide with a molecular mass of 2502 Da was purified to homogeneity using a heparin‐affinity column and C18 reverse‐phase and gel‐permeation high‐performance liquid chromatography. The complete amino acid sequence of misgurin, which was determined by an automated amino acid sequencer, was Arg–Gln–Arg–Val–Glu–Glu–Leu–Ser–Lys–Phe–Ser–Lys–Lys–Gly–Ala–Ala–Ala–Arg–Arg–Arg–Lys. Misgurin is a strongly basic peptide which has 5 arginine and 4 lysine residues. Comparison of the amino acid sequence with those of other known antimicrobial peptides revealed that misgurin was a novel antimicrobial peptide. Misgurin showed a strong antimicrobial activity in vitro against a broad spectrum of microorganisms without significant hemolytic activity and was about 6 times more potent than magainin 2. Scanning electron microscopy confirmed that the peptide caused damage to the cell membrane by a pore‐forming mechanism similar to that of magainin 2. This damage occurred at the minimal inhibition concentration (MIC), but at higher concentration than MIC it lysed the cell.