To study the archaeal diversity of deep-sea sediments in the tropical Western Pacific, we investigated the archaeal community structure in six sediments subsamples along the MD3059 sediment core collected during the IMAGES ⅪⅤ cruise with 16S rDNA analysis. A total of 543 archaeal 16S rDNA clones were examined and a total of 137 OTUs were obtained. Phylogenetic results showed that the archaeal diversity in the collected samples was very diverse, and the obtained OTUs were grouped into Crenarchaeota and Euryarchaeota, with the former dominated by Miscellaneous Crenarchaeotic Group (MCG, 54% of total archaeal clones) and the latter dominated by Marine Benthic Group D (MBG-D), South African Gold Mine Euryarchaeotic Group (SAGMEG) and Marine Benthic Group B (MBG-B). These data have important implications for our understanding of archaeal community in deep-sea sediments of the tropical Western Pacific.