The topology of the tree of Life, and particularly the evolutionary relationship between Archaea and Eukarya, is a major biological issue, with presently two conflicting hypotheses. In the first one, Archaea and Eukarya are sister groups1,2, whereas in the other, Eukarya emerged within Archaea3. The latter hypothesis has been boosted by the reconstruction, from metagenomic data, of three partial genomes from members of a possible new archaeal phylum, Lokiarchaeota. In a phylogenetic tree constructed from the concatenation of 36 universal proteins, Eukarya was shown branching within Lokiarchaeota4. The lokiarchaeota were rapidly presented as the “missing link” between “Prokaryotes” (Archaea) and Eukarya, and a definitive argument supporting the archaeal ancestor scenario for eukaryogenesis3. In reanalyzing the data, we observed that most lokiarchaeal universal proteins branch within Archaea. In one of the minority proteins that branch as sister group to Eukarya, we observed several specific insertions shared between the Loki protein and specific eukaryotic proteins. This suggests that the position of the lokiarchaea in the original analysis is probably biased by reconstructions problems. We proposed a new position for the bona fide Lokiarchaea, based on a robust phylogenetic analysis of the two large RNA polymerase subunits concatenated, and supported by several lines of evidence. Our results clearly show that the Lokiarchaeon is not more the missing link to Eukarya, and supports the classical Woese tree of Life. This shift from one scenario to its opposite clearly shows that the process of eukaryogenesis is still open for debate.