Infectious Salmon Anaemia is a serious disease of farmed Atlantic Salmon on three continents. The disease causes severe anaemia and haemorrphagic liver necrosis, and carries major economic consequences for affected areas. Nevertheless, the causative agent, a novel orthomyxo-like Virus (Infectious Salmon Anaemia Virus - ISAV), is only partially characterized at the molecular level. We report the isolation and characterization of two novel ISAV segments at the genomic and proteomic levels. These segments are the third and fourth largest of the (ISAV) genome and may code for a nucleocapsid protein (NP) and a polymerase (PA). Western blot analysis using an ISAV polyclonal antibody identified one of these novel proteins as being the major tissue antigen. We discuss the implications of our findings for vaccine development and surveillance of Infectious Salmon Anaemia.