The Pacific sockeye salmon Oncorhynchus nerka is a globally important food fish with high environmental significance to the western coastal regions of North America. Piscine orthoreovirus (PRV) and infectious hematopoietic necrosis virus (IHNV) are two viruses known to infect Sockeye and other salmon species and are considered important risk factors in managing cultured and wild salmon populations. The aim of this study was to provide a kidney-specific reference transcriptome for Sockeye salmon and identify genes transcripts with potential responsiveness to PRV, IHNV, or the coinfection thereof.