A molecular assay was designed to distinguish the common sea louse Caligus elongatus from its sympatric relatives. The method identifies the parasites at all developmental stages. Fragments of the mitochondrial Cytochrome C Oxidase 1 (COI) gene from identified adult caligids were amplified by polymerase chain reaction (PCR) and sequenced. Analysis of sequence data from unknown samples permitted identification by clustering of the samples with their appropriate genetic relative. Nucleotide sequences obtained were used for preliminary investigations of the population genetic structure of Caliguselongatus. Aligned sequences from the COI gene from this speciesindicate that our C. elongatus material divides into two distinct clades, possibly revealing two closely related species. The two genotypes do not appear to be associated with sample site, parasite gender, sample time or host species. Parasites from both groups were found on Atlantic salmon (Salmosalar), sea trout (Salmotrutta), pollack (Pollachiuspollachius), saithe (Pollachiusvirens), and Atlantic herring (Clupeaharengus).