Core proteins of mitochondrial protein import are found in all mitochondria, suggesting a common origin of this import machinery. Despite the presence of a universal core import mechanism, there are specific proteins found only in a few groups of organisms. One of these proteins is the Translocase of Outer Membrane 70 (Tom70), a protein that is essential for the import of pre-proteins with internal targeting sequences into the mitochondrion. Until now, Tom70 has only been found in animals and Fungi. We have identified a tom70 gene in the human parasitic anaerobic stramenopile, Blastocystis sp. that is neither an animal, nor a fungus. Using a combination of bioinformatic, genetic complementation and immunofluorescence microscopy analyses we demonstrate that this protein functions as a typical Tom70 in Blastocystis mitochondrion-related organelles. Additionally, we identified putative tom70 genes in the genomes of other stramenopile and a haptophyte, that, in phylogenies, form a monophyletic group distinct from the animal and the fungal homologs. The presence of Tom70 in these lineages significantly expands the evolutionary spectrum of eukaryotes that contain this protein and suggests that it may have been part of the core mitochondrial protein import apparatus of the last common ancestral eukaryote.