Genetic differentiation within the salmon louse Lepeophtheirus salmonis (Krøyer, 1837), was investigated by the sequencing of specific nucleotide regions. Partial sequences of the 18S ribosomal RNA gene and the ribosomal internal transcribed spacer (ITS-1) region from single sea lice were amplified by the polymerase chain reaction (PCR). Lice were collected from wild and farmed Atlantic salmon (Salmo salar L., 1758) from nine selected localities around the Scottish coastline. A 0.9kb fragment of the 18S ribosomal RNA gene was amplified and compared for several samples of lice which showed no observable differences between the lice from different collection sites confirming the absence of cryptic species. The 454 nucleotide ITS-1 sequence showed differences between derived sequences from 13 sea lice samples from 4 collection sites which included 2 farm sites and 2 sites where lice were taken from wild fish. Across all samples, there was a 92.14% similarity in the ITS-1 sequence. The percentage similarity in the ITS-1 sequence in samples of lice from two fish farms were 99.71% (site A) and 95.72% (site D) but only 86.90% (site B) and 86.03% (site C) similarity was shown in lice samples taken from sites where wild salmonids were caught. The greater similarity between the ITS-1 sequence within farm sites may be attributed to a restricted gene flow within lice populations in Atlantic salmon cage sites.