Membrane trafficking pathways play critical roles in Apicomplexa, a phylum of protozoan parasites that cause life-threatening diseases worldwide. Here, we report the first retromer-trafficking interactome in Toxoplasma gondii. This retromer complex is typified by a singular architecture with a trimer Vps35-Vps26-Vps29 core complex that serves as a hub for the known endosome-like compartment (ELC) and parasite-specific proteins. Conditional ablation of TgVps35 revealed that the retromer complex is not only crucial for the biogenesis of secretory organelles, but also for maintaining parasite architecture. The aim of this quantitative experiment was to determine the stoichiometry the trimer involved in the retrograde transport of Toxoplasma gondii.