Over the last two decades, many new groups of deeply branching uncultivated archaea have been unveiled by molecular screening of 16S rRNA genes. Among these, Thaumarchaeota (Brochier-Armanet et al., 2008) are now known to represent a highly diversified and ancient phylum present in a wide variety of ecosystems, including marine and fresh waters, soils and also hot environments (Pester et al., 2011). The Thaumarchaeota have rapidly gained much attention after the discovery that some of them are able to oxidize ammonia aerobically, providing the first example of nitrification in the Archaea and therefore extending the range of microorganisms capable of this important metabolism, which was previously thought to be restricted to a few proteobacterial lineages (Konneke et al., 2005). The interest raised by Thaumarchaeota is witnessed by the growing availability over the last 4 years of isolated representatives (or enrichment cultures) and of genomic data. This opens up a whole new perspective on the diversity of Archaea and on ancient evolution.