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Sponges have rich and diverse associated microbial communities, which may have important functions in their metabolism. A survey of the archaeal communities of 23 poriferan species, focusing on the family Axinellidae, was conducted over the period 2002–2004 using 16S rDNA gene libraries created with archaeal-specific primers. The 28S rDNA sequences of the sponge hosts were also obtained. Of 23 species, 19 showed evidence of archaeal communities from group C1a (marine group I; Crenarchaeota), with three of these also showing evidence of Archaea from group E2 (marine group II; Euryarchaeota). Within the Crenarchaeota, two strongly supported sponge-specific clades were identified corresponding to the sponge family Axinellidae, and a novel sponge clade denoted clade C. These findings suggest that these archaea have evolved closely with their sponge hosts and are likely to play an important role in their metabolism.