Chaperonin is a double ring-shaped oligomeric protein complex, which captures a protein in the folding intermediate state and assists its folding in an ATP-dependent manner. The chaperonin from a hyperthermophilic archaeum, Thermococcus sp. strain KS-1, is a group II chaperonin and is composed of two distinct subunits, α and β. Although these subunits are highly homologous in sequence, the homo-oligomer of the β-subunit is more thermostable than that of the α-subunit. To identify the region responsible for this difference in thermostability, we constructed domain-exchange mutants. The mutants containing the equatorial domain of the β-subunit were more resistant to thermal dissociation than the mutants with that of the α-subunit. Thermostability of a β-subunit mutant whose C-terminal 22 residues were replaced with those of the α-subunit decreased to the comparable level of that of the α-subunit homo-oligomer. These results indicate that the difference in thermostability between α- and β-subunits mainly originates in the C-terminal residues in the equatorial domain, only where they exhibit substantial sequence difference.