Infectious salmon anaemia virus (ISAV) is an orthomyxovirus causing anaemia and circulatory disease with high mortality in farmed Atlantic salmon (Salmo salar). Orthomyxoviruses are unusual as RNA viruses as they replicate in the nucleus and some viral transcripts undergo splicing. The nuclear replication necessitates a tightly controlled nuclear import and export of viral proteins. From ISAV genomic segment 7 two known mRNAs are transcribed; one collinear with the genomic segment, coding for the non-structural protein, and one spliced transcript, S7ORF2, coding for a protein with unknown function. Here we report initial functional analysis of the S7ORF2 protein. The results indicate that S7ORF2 protein gradually accumulates in the host cell during virus replication cycle, locates predominantly in the cytoplasm and is a part of purified virus particles. Trapping of S7ORF2 in the nucleus was obtained by treatment with leptomycin B, an inhibitor of CRM1-mediated nuclear export, indicating that S7ORF2 use CRM1 for the nuclear exit. Immunofluorescent staining of cells over-expressing both S7ORF2 and matrix protein (M) showed co-localization in the nucleus. However, S7ORF2 protein was found to interact with both the viral nucleoprotein (NP) and M proteins in ISAV infected cells as well as in purified viral particles. These results indicate that the S7ORF2 could be called the ISAV nuclear export protein, ISAV/NEP.