Retromer is a complex of proteins that functions in the endosome-to-Golgi retrieval cargo transport pathway. VPS35 works as the central subunit of retromer to recognize the cargos and binds with VPS29 and VPS26 via distinct domains. We show that deficiency of VPS35 or VPS29 accompanies degradation of other subunits, whereas VPS26 deficiency had no effect on VPS29 and VPS35 levels. Although VPS35 forms VPS26–VPS35 and VPS29–VPS35 sub-complexes with similar efficiency in vitro, VPS26–VPS35 was more easily degradable by the ubiquitin–proteasome-system than VPS29–VPS35. These results indicate that VPS29 and VPS35 form a biologically stable sub-complex in vivo.