The deep ocean, one of the largest biomes on Earth, supports diverse microbial communities, which play important roles in biogeochemical cycles. However, despite their importance, viruses in the deep ocean remain largely unknown. In this study, we performed metagenomics to investigate viral communities from deep sea waters in the South China Sea (SCS) and western Pacific Ocean (WPO). Deep-sea viral sequences were largely uncharacterized, and the majority of ‘known’ fractions were homologous to Caudovirales. Although possible sinking of certain upper-ocean viruses (e.g. homologs of cyanophages) to deep sea was observed, deep viromes were distinguished from the surface virome, as evidenced by their significant differences in taxonomic, genomic, and functional diversities. Furthermore, we identified a number of abundant homologs of temperate viruses from deep sea. Compared with surface viruses, in silico annotations showed that deep-sea temperate phages encoded abundant auxiliary functions that were likely involved in viral or host fitness under stressed conditions. This finding implies the probable important roles of lysogeny in the survival and stability of prokaryotes within extreme environments. Collectively, the high abundance of temperate viruses suggests that lysogeny is the preferred mode of existence of deep-sea viruses inhabiting an energy-limited environment. Hence, lysogeny could play a major role in deep-sea ecosystems and global biogeochemical cycling.