Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored fraction of the virosphere. Using meta-transcriptomics, we investigated the viromes of 11 groups of Antarctic fish collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes, aiming to understand the evolutionary trajectories of viruses in these polar species. The continent's shift southward and cooling temperatures over 20 million years ago led to a reduction in biodiversity and subsequent adaptive radiation of marine fauna, particularly of notothenioid (Perciformes) fish. Despite the lower host species richness in polar regions, our study revealed a surprisingly complex virome diversity in Ross Sea fish, comparable to that of fish in more diverse and warmer marine environments. We observed instances of both virus-host co-divergence and host-switching events, particularly among notothenioid fish, suggesting a link between speciation and viral diversity. These findings emphasise the importance of understanding virus-host interactions in response to environmental shifts, especially in less diverse ecosystems vulnerable to the impacts of climate change and human activities.