Atypical Aeromonas salmonicida is frequently associated with disease and mortality in farmed lumpfish (Cyclopterus lumpus L). Challenge experiments using different modes of exposure identified both high and low pathogenic isolates. Intraperitoneal vaccination induced production of high levels of specific antibodies particularly in fish given multiple injections. The immune sera contained antibodies cross reactive with both high and low pathogenic isolates. SDS-PAGE and LC/MSMS analyses showed that the highly virulent isolate expressed the virulence array protein (A-layer) while the less virulent isolate did not. Vaccines, containing the highly virulent isolate, formulated as a monovalent or as a trivalent vaccine, provided 73 and 60 relative percent survival (RPS) respectively, following intraperitoneal challenge. The detection of high levels of specific antibodies in immune sera and the protection provided by the test vaccines strongly indicate that it is possible to vaccinate lumpfish against atypical A. salmonicida and most probably also against other infectious bacterial diseases.