Once in the sea, Atlantic salmon lose their freshwater parasites but acquire others from the marine environment. The variety of parasites may increase for Atlantic salmon in the sea. The sea louse , Lepeophtheirus salmonis, is one of the more common ocean parasites of Atlantic salmon. With severely infested fish, often the skin is loose, and flesh may be exposed. The most important vertebrate parasite is probably the sea lamprey , Petromyzon marinus.
Atlantic salmon are susceptible to numerous bacterial, viral, and fungal diseases.
Furunculosis can be a problem in both the freshwater and marine life stages of Atlantic salmon. It is so widespread that no natural waters with resident fish populations are considered to be free of it. Control measures include commercial vaccines and surface disinfection of eggs with iodophore. Furunculosis can be a source of significant mortality in wild populations if river water temperatures become unusually high for extended periods. Bacterial kidney disease is a chronic infection of salmonine fishes in culture environments.