This study investigates the viral communities in deep-sea seamount sediments in the western Pacific Ocean using a combination of bulk metagenome and virome analyses. The results reveal extensive diversity and previously unknown viral clades, with a significant presence of temperate viruses and auxiliary metabolic genes (AMGs) in virus genomes. The viral communities are highly diverse and show high divergence across different seamounts, likely due to the geographical features of seamounts compromising viral connectivity. The study also highlights the significant roles viruses play in carbon, sulfur, and nitrogen cycling by interacting with dominant prokaryote lineages. The findings provide essential insights into the biogeography and ecological functions of viruses in seamount ecosystems, emphasizing the importance of seamounts as unique and isolated habitats with high levels of endemism.This study investigates the viral communities in deep-sea seamount sediments in the western Pacific Ocean using a combination of bulk metagenome and virome analyses. The results reveal extensive diversity and previously unknown viral clades, with a significant presence of temperate viruses and auxiliary metabolic genes (AMGs) in virus genomes. The viral communities are highly diverse and show high divergence across different seamounts, likely due to the geographical features of seamounts compromising viral connectivity. The study also highlights the significant roles viruses play in carbon, sulfur, and nitrogen cycling by interacting with dominant prokaryote lineages. The findings provide essential insights into the biogeography and ecological functions of viruses in seamount ecosystems, emphasizing the importance of seamounts as unique and isolated habitats with high levels of endemism.