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The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, “Lokiarchaeota”, from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life. Strikingly, removal of a single protein, the elongation factor EF2, is sufficient to break the Eukaryotes-Lokiarchaea affiliation. Our analysis suggests that the three lokiarchaeal EF2 proteins have a chimeric organization that could be due to contamination and/or homologous recombination with patches of eukaryotic sequences. A robust phylogenetic analysis of RNA polymerases with a new dataset indicates that Lokiarchaeota and related phyla of the Asgard superphylum are sister group to Euryarchaeota, not to Eukarya, and supports the monophyly of Archaea with their rooting in the branch leading to Thaumarchaeota., Author summary Two scenarios have been proposed to describe the history of cellular life on our planet. For some authors, two lineages emerged from the last universal cellular ancestor, one leading to Bacteria, the other one leading to a common ancestor of Archaea and Eukarya (Woese’s hypothesis), while others suggest that Eukaryotes emerged from within an archaeal subgroup (eocyte hypothesis). This latter hypothesis has been boosted by the reconstruction of new archaeal genomes from environmental DNA. These analyses have suggested that eukaryotes originated from complex archaea, called Lokiarchaeota, the first described members of the recently proposed Asgard superphylum. Considering the importance of this question, we performed new analyses of the universal proteins from Lokiarchaea and realized that their affiliation to Eukaryotes was most probably due to different biases, including chimeric sequences and unequal rate of protein evolution. From our results, we suggest here that Lokiarchaea and close relatives are sister group to Euryarchaeota, not to Eukarya. Notably, we also show that the choices of the universal markers to include in one’s analysis will critically impact the scenario supported and that some markers as the RNA polymerase support the traditional Woese’s tree.