Caligus rogercresseyi, a marine ectoparasite, causes notable economic losses for the Chilean salmonid industry. Nevertheless, the immunological responses of infected fish remain poorly understood, including proinflammatory cytokine generation and the respective modulatory effects of various cytokine receptors. This study evaluated mRNA expression of the NLRC5, major histocompatibility complex (MHC) class II, I-kappa-B-alpha, a regulatory that inhibits NF-kappa-B, and proinflammatory cytokines (IL-1β and IL-18) in the liver and muscle of Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynchus kisutch) during a time-course C. rogercresseyi infestation trial. All assessed mRNA were strongly regulated during infestation, but S. salar showed up-regulated expression, possibly accounting for the high infestation vulnerability of this salmonid. In conclusion, this work helps to understand the modulation of the expression of different transcripts involved over short periods of C. rogercresseyi infestation in two salmonid species (S. salar and O. kisutch).