Although oligotrophic, abyssal marine sediments cover most of the sea bottom, previous investigations of microbial diversity have primarily focused on organic-rich, anoxic sediments of continental margins. In contrast, abyssal open-ocean sediments are oxidized and contain limiting organic substrate concentrations. This study examines the archaeal diversity of oligotrophic, oxic and nitrate-reducing marine sediments and oxic bottom water in the South Pacific Gyre. 16S rDNA clone library analysis identified phylogenetically distinct lineages of the Marine Group I (MG-I) Crenarchaeota in oxidized sediment that are different from those in bottom water. Thus, the sediment habitat selects for different MG-I lineages, within short vertical distances of a few centimetres.