While the archaeal domain of life was discovered more than 30 years ago, the biology of archaeal organisms remains to be relatively obscure, especially when compared to that of bacterial and eukaryotic life. Yet, despite the limited knowledge regarding their lifestyle and ecological relevance, evidence is mounting that certain archaea play key roles in global nitrogen and carbon cycles. In addition, archaea share a common branch in the tree of life with the eukaryotes, and have most likely played a prominent role in the emergence of the eukaryotic cell, and thus of complex life. Interestingly, recent ecological surveys have started to reveal a hidden diversity of archaeal life. The exploration of this supposed ‘archaeal dark matter’ might thus hold relevance for a number of fundamental issues and reveal profound insights about the diversity, ecology and evolution of the archaeal domain of life. Unfortunately, characterization of these uncultured lineages is procrastinated by limitations in cultivation techniques and limited availability of genetic tools, urging for the exploration of alternative strategies to do so.Here I am proposing to utilize a single-cell phylogenomics approach to explore novel archaeal lineages at the genomic level. Habitats hosting novel archaea will be sampled and single-cell genome sequencing will be performed using next-generation sequencing technology. The proposed strategy will result in (1) obtaining a better sampling of archaeal genomes, (2) gaining insight in the evolutionary history of the archaeal domain of life through phylogenomics, and (3) obtaining information regarding the biology and lifestyle of these novel archaeal lineages. This work will dramatically increase the number of archaeal genomes available in public databases for both researchers studying the physiology of archaea in different environments and also for evolutionary biologists tracing the evolutionary history of the three domains of life.