Recent studies demonstrated that endosomal transport played important roles in various plant functions. The RAB GTPase regulates the tethering and fusion steps of vesicle trafficking to target membranes in each trafficking pathway by acting as a molecular switch. RAB GTPase activation is catalyzed by specific guanine nucleotide exchange factors (GEFs) that promote the exchange of GDP on the RAB GTPase with GTP. RAB5 is a key regulator of endosomal trafficking and is uniquely diversified in plants; the plant-unique RAB5 group ARA6 was acquired in addition to conventional RAB5 during evolution. In Arabidopsis thaliana, conventional RAB5, ARA7 and RHA1 regulate the endosomal/vacuolar trafficking pathways, whereas ARA6 acts in the pathway from the endosome to the plasma membrane. Despite their distinct functions, all RAB5 members are activated by the common GEF VACUOLAR PROTEIN SORTING 9a (VPS9a). VPS9a consists of an N-terminal conserved domain and C-terminal region (CTR) with no similarity to known functional domains. In this study, we investigated the function of the CTR by generating truncated versions of VPS9a and found that it was specifically responsible for ARA6 regulation; moreover, the CTR was required for the oligomerization and correct localization of VPS9a. The oligomerization of VPS9a was mediated by a distinctive region consisting of 36 amino acids in the CTR that was conserved in plant RAB5 GEFs. Thus the VPS9a CTR plays an important role in the regulation of the two RAB5 groups in plants.