Aquaculture is a leading sector in providing sufficient high-quality protein for a growing world population, and the need for increased, year-round production has seen a rise in land-based recirculating aquaculture systems (RAS). Atlantic salmon is a valuable cultured species with a complex life cycle which requires growth in freshwater (FW) and seawater (SW). The first weeks post-SW-transfer (SWT) are often accompanied by high mortality rates. Little is known about how FW rearing history (e.g. RAS vs traditional open water systems) impacts post-SWT mortality. In this study we investigate the transcriptomic response during a viral stimulation two weeks post-SWT in fish reared in either FW RAS or open loch systems.