Atlantic cod farming experiences renewed growth in Norway, and increased awareness is essential to address emerging diseases in this species. There are few reports on gill diseases in cod, and to date, no viral gill infections of cod have been documented. In this study, we collected samples from three sequential time points in summer 2023 from farmed cod suffering from cardiorespiratory disease. We document severe heart and gill pathology, and a novel double-strand DNA virus was discovered in the gills. Through comprehensive genetic characterisation and comparative sequence analysis, this virus was classified as a new species in the genus Poxvirus, designated cod gill poxvirus (CGPV). We demonstrate disease causality with severe gill lesions as shown by histopathology and RNA scope in situ hybridisation, and poxvirus particles were identified in gill epithelial cells by transmission electron microscopy. Further, another gill pathogen not previously described in cod, Candidatus. Branchiomonas cysticola, was identified by pcr and in situ hybridisation. Our findings provide strong evidence for poxvirus in Atlantic cod and underscore the imminent threat posed to Atlantic cod farm industry.