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Salmon alphavirus (SAV) is a widespread virus that infects Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) in Europe. It has a fatality rate of ≤48% and can cause pancreatic and sleeping disease. With the frequent exchange of salmon farming trade, it may become a global pathogen; therefore, a sensitive, effective, and high-throughput detection method is necessary. The serological diagnoses for SAV are indirect immunofluorescence assays (IFA) and indirect enzyme-linked immunosorbent assays (ELISA), which can only detect one of the six subtypes of SAV. In this study, an insect cell/baculovirus expression system was used for simultaneous detection of multiple genotypes (SAV1, SAV2, and SAV5) and an indirect double-antibody sandwich-enzyme linked immunosorbent assay (IDAS-ELISA) method was adopted, based on the highly conserved region (E1) of SAV1-6. The results showed that the IDAS-ELISA had no cross-reaction with other common RNA viruses and high sensitivity with 103.4TCID 50 /0.1 mL detection line. SAV 1 (98.33%) and SAV 2 (91.67%) samples were positively identified by IDAS-ELISA and real-time polymerase chain reaction (PCR), respectively. This assay can simultaneously detect multiple subtypes of SAV and provide technical support for clinical diagnosis and the epidemiology of SAV. • An IDAS-ELISA was established to detect multiple SAV genotypes. • Bac-to-Bac system was used to prepare SAV E1 positive products due to its high safety and high protein content. • This assay has high specificity and sensitivity, and is suitable for the diagnosis and control of SAV infection. [ABSTRACT FROM AUTHOR]