Aquatic viromes comprise a vast array of viral classes that inhabit aquatic ecosystems, ranging from oceans to aquaculture operations. Such diversity of bacteria plays a significant role in the ecology of microbes, the cycling of nutrients, and the changing dynamics of aquatic environments. Viruses are infectious agents that pose a serious threat to the aquaculture sector, triggering disease outbreaks that can result in significant economic losses and have a negative impact on global seafood productivity. Studying viromes through metagenomic research presents breakthrough prospects for the fisheries sector to address challenges in disease control, sustainable aquaculture, and environmental surveillance. Exploring metagenomic research also promises a transformational approach for overcoming such challenges by gathering more information about host-virus interactions, viral diversity, and disease evolution. It has the potential to monitor viral populations, which aids in environmental surveillance by maintaining ecosystem stability and limiting the threat of virus transmission between farmed and wild aquatic populations. Incorporating viromics into aquaculture research may aid the industry in shifting to sustainable and more resilient production systems, reducing losses while enhancing ecosystem health and food security. This chapter delves into the notion of aquatic viromes, the applications of metagenomics in revealing viral diversity, and their relevance for establishing fisheries research, as well as aquaculture techniques.