To study the archaeal community structure and diversity, clone libraries were constructed from water samples of the KX08-973-22 site（named CWP）in the core area of west Pacific Warm Pool by using the 16S rDNA library technology. Finally, 561 clones were obtained and 50 operational taxonomic units (OTUs) were identified after analysis. By homologous comparing for the 16S rRNA gene sequences, constructing phylogenetic tree and statistical analysis, we obtained the following results: all the archaeal phylotypes in this study were affiliated with Euryarchaeota and Crenarchaeota, respectively. For the Euryarchaeota, Marine Group II (MGII, 49.0%) were the most predominant phylotypes and marine group III (MGIII) only accounted for 5.7% of the libraries. For the Crenarchaeota, marine group I（MGI） dominated the clone libraries, and Miscellaneous Crenarchaeotic Group (MCG, 0.2%) constituted a small proportion of the libraries. Our study suggested that archaeal phylotypes from the core surface area of the west Pacific Warm Pool were not high diversity and community structure showed stratification within small vertical distances