The lack of organisation of monophyletic lineages in the phylogeny and taxonomy of the group formerly known as protists has precluded the understanding of the group’s evolutionary history and trait comparison among members of the group. We used a phylogenomic approach to establish phylogenetic hypotheses of this group of organisms. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences with previous published ones, but some unexpected phylogenetic relationships were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade was recovered as polyphyletic. We failed to recover a monophyletic Excavata group, most likely because of longbranch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject relationships in previous hypotheses. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two species, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found. We discuss the relative positions of the Alveolata and Stramenopila groups, the latter being of special interest in our research group. © 2016. Acad. Colomb. Cienc. Ex. Fis. Nat. All rights reserved.