Parasitism can affect every aspect of wildlife ecology, from predator avoidance and competition for food to migrations and reproduction. In the wild, these ecological effects can have implications for host fitness and parasite dynamics. In contrast, domestic environments are typically characterised by high host densities, low host diversity, and veterinary interventions, and are not subject to processes like predation, competition, and migration. When wild and domesticated hosts interact via shared parasite populations, understanding and predicting the outcomes of parasite ecology and evolution for wildlife conservation and sustainable farming can be a challenge. We describe the ecology and evolution of ectoparasitic sea lice that are shared by farmed and wild salmon and the insights that experiments, fieldwork, and mathematical modelling have generated for theory and applied problems of host–parasite interactions over the course of a long-term study in Pacific Canada. The salmon–sea lice host–parasite system provides a rich case study to examine the ecological context of host–parasite interactions and to shed light on the principal challenges of parasite management for wildlife health and conservation.