Eukaryotes are thought to have arisen via the engulfment of a proto-mitochondrion by an archaeon, suggesting that many features of the eukaryotic cell were present in the archaeal ancestor. However, known archaea lack certain eukaryotic hallmarks of cellular complexity, such as an endomembrane system and the means to phagocytose a proto-mitochondrion. In this study, Spang et al. sequenced uncultivated metagenomes from a deep sea vent and discovered one complete and two partial novel archaeal genomes that constitute the new candidate phylum 'Lokiarchaeota'. The predicted proteome of these novel archaea contains homologues of many eukaryotic proteins that function in the endomembrane system and in phagocytosis, including actin and related proteins, and Ras superfamily GTPases, suggesting that this phylum provides the missing link in eukaryogenesis.