Many fishes produce a repertoire of positively charged antibacterial peptides as part of innate immunity to bacterial invasion. Based on their biochemical and structural properties, fish antibacterial peptides can be classified into four types: amphipathic or hydrophobic α-helical peptides without cysteine; β-sheet peptides with several disulfides bonds; histone-like proteins and glycoproteins. Despite significant variations in length and composition, a common feature of fish antibacterial peptides is that they all have special structures which allow them to bind or disturb the membrane of bacteria in millimolar concentrations. Fish antibacterial peptides are predicted to be translated as prepropeptides that undergo proteolytic cleavage of amino-terminal hydrophobic signal and carboxy-terminal acidic portion to form the mature peptides. Heretofore, several fish antibacterial peptide genes have been cloned and sequencing analyses revealed that most of them were comprised of an open reading frame with four exons and three introns and the upstream region with some consensus binding sequences for transcription factors found in other fish functional genes. Recent data suggest that the details of the antibacterial pathways may vary for different peptides and are assigned to different mechanisms. Some may kill bacteria by forming transmembrane ion channels according to the ‘barrel-stave’ mechanism, and some by disrupting membrane according to the ‘carpet-like’ mechanism. In addition, alternative mechanisms, which include their binding to DNA and their interference with DNA or protein synthesis, have been proposed to explain the antibacterial action of several peptides. The study of fish antibacterial peptides may improve the understanding of peptide-mediated host defence.