It is recognized that archaea constitute a significant portion of global biomass. Examining the distribution of microorganisms in submarine canyons presents an opportunity to study the association of microbial dynamics relating to continental-oceanic interactions. Here we investigated archaeal communities along a sediment column over glacial-interglacial cycles in the Pearl River submarine canyon in the northern South China Sea. This study was aimed at determining the vertical distribution of benthic archaea, evaluating their ecological importance in subseafloor biosphere.