Cardiomyopathy syndrome (CMS) caused by piscine myocarditis virus (PMCV) has emerged with the rise of the aquaculture of Atlantic salmon (). The lack of cell culture cultivation has hampered the study of this infection. In this study, samples from naturally PMCV-infected Atlantic salmon from different commercial farms were collected and used. In situ hybridization (ISH) revealed intense staining of PMCV RNA in myocardial cells in the spongiform layer of the heart ventricle but almost no staining in the compact layer. In the kidneys, only sporadic staining was seen. Viral RNA was present in all organs, with the highest loads in the heart, kidney, and spleen. The high viral PMCV RNA loads in the heart were due to extensive viral mRNA transcription. The high ratio of viral mRNA to viral genomic dsRNA indicated active transcription but limited production of new viral particles. This suggests that the histopathological changes in the heart are caused by viral mRNA and corresponding viral proteins and not by virus particle formation. The production of full-length transcripts is regulated, with a reduction in the relative number of ORF3-containing transcripts at high transcription rates. Efforts to identify alternative hosts, such as fungi, were inconclusive, as fungal sequences were found inconsistently in the salmon tissue samples. The results of this study reinforce the need for further research to fully understand PMCV's life cycle and potential alternative hosts and its whereabouts when it is not infecting the hearts of the Atlantic salmon.