Atlantic salmon populations across the world have diverse ecological and evolutionary histories, from wild anadromous or landlocked, to domestication and genetic modification. The natural host behaviours confer protection from infestation by ectoparasitic salmon lice Lepeophtheirus salmonis, yet whether genetic origin results in different behaviours and thus susceptibility to infestation is unknown. In common garden experiments, we tested antiparasite behaviours, susceptibility and retention of salmon lice in wild anadromous, wild landlocked, domesticated and genetically modified domesticated strains. Within domesticated strains, we tested two infestation histories (previously infested and naïve) and a new phenotype (albino colouring). Farmed stocks initially acquired 24%-44% higher levels of parasite density than the wild and landlocked strains. Burst swimming and displacement behaviours were higher in the domesticated groups, and jumping was more prevalent in the domesticated strains. At 34 days post-infestation, domesticated strains and the wild anadromous strain did not differ significantly from each other; however, landlocked salmon had increased infestation levels considerably. Domesticated strains lost ~20% (±9.9%-16.5%; 95% CI) of their initial parasite load, while parasite load increased by 5.5% (±30.1%) for wild salmon and 20.1% (±28.5%) in landlocked salmon. This study provides early evidence for diverged host-parasite interactions associated with domestication in this system.