Marine farmed Atlantic salmon (Salmo salar) are repeatedly susceptible to amoebic gill disease (AGD) caused by the ectoparasite Neoparamoeba perurans over their life cycle. The parasite elicits a highly localized response within the gill epithelium mucosa resulting in multifocal mucoid patches at the site of parasite attachment. This host-pathogen response drives a complex immune reaction within the pathology of the disease, which remains poorly understood. A dual RNA-seq approach was employed using Illumina sequencing technology to investigate both the linteraction between the host and the parasite. Overall design: A multi-tissue transcriptomic data set was generated from the gill (including both lesioned and non-lesioned tissue), head kidney and spleen tissues of AGD unaffected (n=4) and affected Atlantic salmon (n=4).