Ammonia-oxidizing archaea is one of the most abundant microbial groups driving the nitrogen cycling on Earth. Especially, in the deep sea, its relative abundance can reach 20%-40% of the total prokaryotes. However, the lack of deep-sea ammonia-oxidizing archaea isolates hindered our comprehensive understanding of their physiology and ecological contribution. In this paper, we analyzed the relationship between characteristics of deep-sea environments and the adaptability of microorganisms, focusing on the potential survival strategies and metabolic preferences of deep-sea ammonia-oxidizing archaea. This knowledge will assist us to design suitable cultivation techniques on them. Moreover, the ammonia-oxidizing archaea habituated in the deep sea apparently distanced from those in soil or surface ocean, in terms of phylogeny as well as physiology. Therefore, we are about to reconsider the global oceanic nitrogen budget estimation.