Six eukaryotic supergroups have been proposed based on both morphological and molecular data. However, some of these supergroups are contentious and the deep relationships among them are poorly resolved. This is due to a limited number of morphological characters and few molecular markers in current use. The lack of resolution in most multigene analyses, including phylogenomic analyses, necessitates a search for additional, appropriate molecular markers to enable targeted sampling of taxa in key phylogenetic positions. We evaluated the phylogenetic signal of 860 proteins obtained from the Clusters of Orthologous Groups of proteins (COGs) database. We report a total of 17 markers that resulted in well-resolved topologies that are congruent with well-established components of the eukaryotic tree. To establish their utility, we designed universal degenerate primers for six markers, some of which showed promising results in unicellular eukaryotes. Finally, we present phylogenetic informativeness profiles for seven selected markers, revealing that the markers contain phylogenetic signal that spans the whole tree including the deeper branches.