Apicomplexan parasites cause numerous diseases in humans and animals, including malaria (Plasmodium species) and toxoplasmosis (Toxoplasma gondii). Despite being a major drug target, the protein composition of the coenzyme Q:cytochrome c oxidoreductase complex (Complex III) in these parasites was previously unknown. Our work highlights the divergence of mitochondrial ETC Complex III composition in apicomplexan parasites and provides a broader understanding of Complex III evolution. Our study also provides important insights into what sets this major drug target apart from the equivalent complex in host species. Future studies can build on our findings to reveal how novel subunits contribute to Complex III function to further investigate this important drug target.