Scygonadin is a novel antimicrobial peptide, which was originally isolated from the seminal plasma of the mud crab, Scylla serrata. Based on the partial 20-residue NH(2)-terminal sequence of the peptide, H-Gly-Gln-Ala-Leu-Asn-Lys-Leu-Met-Pro-Lys-Ile-Val-Ser-Ala-Ile-Ile-Tyr-Met-Val-Gly-OH, scygonadin was cloned from the gonads of S. serrata using a degenerated reverse transcriptase (RT)-PCR and rapid amplification of cDNA ends (RACE). The full-length cDNA sequence contains an open reading frame of 539 bases (excluding polyA) with a coding capacity of 126 amino acids, which constitutes a putative NH(2)-terminal signal sequence (1-24) and a mature peptide (25-126). Analysis of the genomic DNA sequence revealed that scygonadin consists of 2300 bp containing two introns (1569 and 120 bp) and three exons (187, 131 and 218 bp) and this sequence is different from any other reported antimicrobial peptide. The theoretical pI of the mature peptide is 6.09, which suggests that it is an anionic molecule. The sex and tissue-specific expression of the scygonadin gene was revealed using RT-PCR and Northern-blot analysis of multiple tissues of S. serrata males and females and this demonstrated that the scygonadin gene was predominantly expressed in the male reproductive tract of S. serrata and was restricted to the ejaculatory duct. This suggests that scygonadin might be one of the antibacterial peptides responsible for protection of the male crab reproductive tract from invading pathogenic microorganisms, so as to maintain a sterile environment leading to successful fertilization.