The study of biogeographic distribution patterns and the processes that provoke them helps to understand the generation and maintenance of the biodiversity of macro- and microorganisms. Although Bacteria and Archaea are major components of the marine environment from the surface to the deep ocean, their biogeographic distribution patterns have been mostly studied in surface waters. We studied the abundance and diversity patterns of a functional gene, the amoA gene of Archaea, encoding for ammonia monooxygenase, a key enzyme for nitrification, throughout the Atlantic. Our results point to a niche specialization of two groups of archaeal ammonia oxidizers (AOA) according to ammonia availability, and to the bipolar distribution of AOA down to the bathypelagic realm.