Archaea are abundant in polar oceans but important ecological aspects of this group remain enigmatic, such as patterns of diversity and biogeography. Here, we provide the first high-throughput sequencing population study of Antarctic archaea based on 198 bp fragments of the 16S rRNA gene, targeting different water masses across the Amundsen and Ross Seas. Our results suggest that archaeal community composition is strongly shaped by hydrography and significantly influenced by environmental parameters. Archaeal communities from cold continental shelf waters (SW) of the Ross Sea were similar over depth with a single thaumarchaeal phylotype dominating Antarctic surface waters (AASW) and deeper SW (contributing up to 80% of reads). However, this phylotype contributed less than 8% of reads in circumpolar deep waters (CDW). A related thaumarchaeon (98% identity) was almost absent in AASW, but contributed up to 30% of reads in CDW, suggesting ecological differentiation of closely related phylotypes. Significantly higher archaeal richness and evenness were observed in CDW, with Shannon indices (c. 2.5) twice as high as for AASW, and high contributions of Group II Euryarchaeota. Based on these results, we suggest that CDW is a hotspot of archaeal diversity and may play an important role in the dispersal of archaeal phylotypes to other oceanic water masses.