Cathelicidins are antimicrobial peptides (AMP) belonging to the innate immunity system with host defensive activity against pathogenic microorganisms. The Atlantic cod has been shown to lack a fundamental part of the adaptive immunity system as it is understood today, the MHC II locus. Therefore it is of interest to explore the innate immunity system in cod. A thorough sequencing of the locus encoding Cathelicidin in individuals cought at various locations from around the distributional range reveals a unique pattern of variation. We found two divergent genes (codCath1 and codCath2) each having multiple allelic variants. Alleles of codCath2 also are found in the closest relatives of cod, Gadus ogac, Gadus magrocephalus, Theragra chalcograma and Boreogadus saida. Non-synonymous amino acid substitutions are found both in the conserved part of the protein and in the variant 3´ exon which comprises the active peptide. All major protein structure known for AMP in marine organisms are found in this sole protein of cod. I will discuss the results in terms of evolution of the locus and the evolutionary forces shaping the patterns.