Protein dimerization plays an important role in many cellular biological activities, such as activated enzymes, membrane protein receptors, signaling factors, and transcription factors. Therefore, controlling protein dimerization helps to prevent these biological processes. In this study, the molecule curcubit[8]uril was used to manage the dimerization of protein consisting of the-ala-gly motif at the N-terminus. The CFP/YFP protein pair containing the phe-ala-gly fusion motif was generated using an auto cleavage intein system. The Curcubit[8]uril molecule that induces dimerization of the CFP/YFP protein containing the phe-ala-gly motif was evaluated by FRET (fluorescnt resonance energy transfer) technique. The FRET ratio of 525 nm/475 nm increased significantly from 0.5 to 1.2 in the presence of curcubit[8]uril, which means that this molecule is capable of inducing the dimerization of CFP and YFP proteins bearing the phe-ala-gly motif. Control of protein dimerization by curcubit[8]uril can potentially control biologically functional proteins containing the phe-ala-gly fusion motif.