Susceptibility among salmonids to the ectoparasite Lepeophtheirus salmonis is related to inflammatory reactions at the site of parasite attachment. Salmon from two susceptible (Salmo salar, Oncorhynchus keta) and one resistant (Oncorhynchus gorbuscha) species were exposed to adult L. salmonis. After 24 and 48h, skin samples directly below the attachment site and at non-attachment sites were assessed for transcriptomic profiles of select innate defense genes. Abrasion of the skin permitted comparisons between abrasion-associated injury and louse-associated injury. Infection responses were consistently higher than those caused by abrasion. Temporal patterns of expression were evident in all species for the transcription factor CCAAT/enhancer-binding protein β (C/EBP-β), the cytokine interleukin-6 (IL-6) and the enzyme prostaglandin D synthase (PGDS) at attachment sites. O. gorbuscha was the highest responder in a number of genes while there was an absence of C-reactive protein (CRP) gene expression in S. salar and O. keta, indicating an altered acute-phase response. Moreover, O. keta displayed distinct interleukin-8 (IL-8) and serum amyloid P (SAP) responses. Impaired genetic expression or over-expression in these pathways may be evidence for species-specific pathways of susceptibility to the parasite. At L. salmonis attachment sites, reduced expression compared to non-attachment sites was observed for C/EBP-β (S. salar), CRP (S. salar), SAP (S. salar, O. gorbuscha, O. keta), PGDS (S. salar, O. gorbuscha, O. keta), and major histocompatibility class II (MH class II, S. salar), suggesting local immunodepression.