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Heart and skeletal muscle inflammation (HSMI) caused by Piscine orthoreovirus (PRV) was first described in farmed Atlantic salmon in Chile in 2011. However, as PRV induces long-lasting infections, it is not known when Chilean farmed salmon may have started to show PRV positivity. This study aimed to evaluate the presence/absence of PRV-1 in formalin-fixed, paraffin-embedded Atlantic salmon heart tissues (FFPE) cultured in Chile during 1992 and 1999. The most frequent histopathological findings in the 42 FFPE blocks were mild focal cardiomyocyte degeneration (57.1%) and a mild focal mononuclear inflammatory infiltrate (21.4%) in the ventricular stratum spongiosum of the heart. One of the 42 heart samples analyzed by RT-qPCR was positive for PRV-1 (2.4%). All samples were negative for other viral and bacterial pathogens that can induce similar histological changes in the heart. Taken together, our results show that PRV-1 has been present in Chile—as a low-virulence genogroup—since at least 1994, 17 years before the first HSMI outbreak in 2011. Finally, archaeovirology can be a valid alternative to contribute to the understanding of the epidemiology of diseases in aquaculture.