The Archaea represent the Third Domain of Life and comprise a group of microorganisms that are important players in major biogeochemical cycles. Yet, even though more than 30 years have passed since their discovery, the biology, lifestyle and diversity of the archaeal domain of life remain to be poorly understood thus far, especially when compared to that of Bacteria and eukaryotes.Recent environmental surveys have revealed the existence of a vast, uncultured archaeal diversity, and the characterization of this so called “archaeal dark matter” is of great significance for understanding the diversity, biogeography and ecological relevance of Archaea in general, and the evolution of cellular life on Earth in particular. Yet, efforts to do so have been hampered by difficulties to cultivate these archaeal lineages under laboratory conditions.The current project aims to employ powerful, cultivation-independent approaches to genomically probe several deeply-branching archaeal lineages in order to set genomic standards for quantifying and defining archaeal taxonomic units, to determine molecular signatures of archaeal genomes, to reveal potential ecological functions of uncultivated archaea and to shed new light on the evolutionary relationship between Archaea and Eukaryotes. By combining state-of-the-art single cell genomics and metagenomics workflows with cutting-edge next-generation sequencing and bioinformatics pipelines, genomic data of several deep archaeal lineages will be generated and analyzed, focusing on the enigmatic Korarchaeota, as well as of representatives of the deeply-rooting Deep Sea Archaeal Group (DSAG) and the Ancient Archaeal Group (AAG). The proposed phylogenomic and comparative genomic analyses of these genomic datasets will reveal important novel insights into the enigmatic archaeal domain of life.