Caligid copepods, also called sea lice, are common ectoparasites of wild and farmed marine fish. The salmon louse Lepeophtheirus salmonis (Krøyer, 1837) has emerged as a serious problem for salmon farming in the Northern hemisphere. The annual cost of sea lice to the global salmon mariculture industry has been estimated at €300 million, of which the majority accounts for the cost of chemically treating the farmed salmon. Two L. salmonis laboratory strains, established from field isolates and differing in susceptibility to emamectin benzoate EMB were used in the current study. The aim of the present study was to identify sex-linked and strain-linked genomic polymorphisms in L. salmonis. Salmon lice were exposed to chronic levels of EMB using standard in vitro bioassay methods and sampled at the point where a phenotypic response to exposure was recorded. This strategy facilitated the selection of salmon lice with differing degrees of EMB susceptibility from homogeneous populations such as long-term laboratory-maintained strains. Restriction site associated DNA (RAD) sequencing was used for Single Nucleotide Polymorphism (SNP) identification between salmon louse strains and gender. RAD sequencing (RAD-seq) generated total, 331,642,960 raw reads (101 nt long), that comprised 165,821,480 paired-ended reads although 264,343,660 raw sequence reads remained after filtering. The identification of strain-linked and sex-linked genomic polymorphisms may provide a tool for determining the genetic sex and EMB resistance of salmon lice, and could be useful in the development of alternative control strategies. [Stephen Carmichael, PhD These: https://hdl.handle.net/1893/19526]