Using the selective host-guest inclusion of G2[naphthalene disulfonate], the structural isomers of 1,2-dibromobenzene and 1,3-dibromobenzene were separated. As such, 1,3-dibromobenzene was selectively included as guest into the host framework in mixture isomers over 30% fraction of 1,3- dibromobenzene (X1,3-DBB=0.3) whereas 1,2-dibromobenzene as guest was selective to the inclusion below X1,3-DBB=0.3. This was due to the selectivity of host framework toward the guest molecules playing a role of template to the host framework. From the powder pattern XRD of inclusion compounds crystallized in pure isomer and mixture solutions, the template roles of guest molecules to the host framework were confirmed. Using the DSC, it was found that the more energy was required to release 1,3-dibromobenzene of guest from the host framework than 1,2-dibromobenzene due to the higher thermal stability. The thermal stability of the G2NDS-1,3-dibromobenzene inclusion compound was consistent with the high selectivity of 1,3- dibromobenzene to the host framework in broad range of fraction in the isomer mixture.