Piscirickettsiosis is the most challenging disease present in the Chilean salmon industry. The aim of this study was to describe the expression of genes associated with immune response of Atlantic salmon intraperitoneally infected with LF-89 and EM-90 Piscirickettsia salmonis and vaccinated with inactivated whole-cell bacterin of P. salmonis. The fish infected with PS-LF-89 showed an anti-inflammatory response, whereas this finding was not observed in the PS-EM-90-infected fish and vaccinated fish. Fish infected with both P. salmonis isolates showed mhc1-mhc2, cd4-cd8b and igm overexpression, suggesting that P. salmonis promotes a T CD4(+) and T CD8(+) cell response and a humoral immune response. The vaccinated-fish exhibited mhc1, mhc2 and cd4 overexpression but a significant downregulation of cd8b and igm, suggesting that the vaccine supported the CD4(+) T-cell response but did not induce an immune response mediated by CD8(+) T cells or a humoral response. In conclusion, the expression pattern of genes related to the humoral and cell-mediated adaptive immune response showed upregulation in fish infected with P. sabnonis and down-regulation in vaccinated fish. The results of this study contribute to our understanding of the immune response against P. salmonis and can be used in the optimization of SRS prevention and control measures.