Infectious salmon anaemia virus (ISAV) is a pathogen of consequence to farmed Atlantic salmon, Salmo salar L. ISA control centres on active surveillance for early detection by reverse transcription polymerase chain reaction (RT-PCR), indirect fluorescent antibody assay (IFAT) and virus isolation. Because diagnostic test performance varies among populations and laboratories, the Office International des Epizooties (OIE) recommends an evaluation of test accuracy in each region of use. This is complicated in Maine, USA by the co-existence of ISAV genotypes homologous to North American (NA) and European (EU) isolates. While NA ISAV genotypes isolated in Maine are characterized by high morbidity and mortality, the single EU genotype in Maine has not yet been linked to disease or isolated by cell culture. Consequently, distinguishing among genotypes is critical to infection response. Accuracy in NA genotype detection was estimated from ISA surveillance data using latent class models. Results suggested that RT-PCR is an excellent screening test for NA ISAV genotypes in Maine, although probably with reduced specificity in the presence of EU genotypes. IFAT, in contrast, was a poor screening test for detection of ISAV in Maine, although it may be useful in confirmation of NA genotypes during disease outbreaks.J Fish Dis. 2008 Feb31(2):117-25. Gustafson L, Ellis S, Bouchard D, Robinson T, Marenghi F, Warg J, Giray C. USDA APHIS Veterinary Services, ISA Programme,Eastport,ME,USA.lori.l.gustafson@aphis.usda.gov.