Trypsins constitute a subclass of the S1A family of serine peptidases found in all groups of animal and some bacteria. At present, no information about the genomic organisation of trypsins is available for copepods. The only data of copepod trypsins indicate several different trypsins in the marine parasitic copepod Lepeophtheirus salmonis. In the present study, 31.7 kbp of genomic DNA surrounding the previously described LsTryp1-5 sequences was sequenced. The sequenced regions contain nine full-length and three partial trypsin genes. A conservative estimate based on PCR analysis and genomic sequence indicated at least 22 different trypsin genes in L. salmonis, of which 18 are most similar to the previously described LsTryp1 and -2 cDNA sequences. Four of these genes are putative pseudogenes. In addition, a putative mariner like transposase gene was identified. The genomic sequences suggest that the L. salmonis trypsin genes reside within one or more gene clusters. Three different LsTryp intron exon structures were identified, and all three are different from the intron exon organisation previously reported for other S1A peptidases. This implies several intron loss and gain events in the evolution of the L. salmonis trypsin genes.