Protozoan isolates from the gills of marine-reared Atlantic salmon Salmo salar smolts were cultured, cloned and 8 dominant isolates were studied in detail. The light and electron-microscopical characters of these isolates were examined, and 7 were identified to the generic level. Structure, ultrastructure, a species-specific immunofluorescent antibody test (IFAT), and PCR verified the identity of the Neoparamoeba sp. isolate. Five other genera of amoebae, comprising Platyamoeba, Mayorella, Vexillifera, Flabellula, and Nolandella, a scuticociliate of the genus Paranophrys, and a trypanosomatid (tranosomatid-bodonid incertae sedis) accompanied Neoparamoeba sp. in the gills.