Although messenger mediated spectroscopy is a widely-used technique to study gas phase ionic species, effects of messengers themselves are not necessarily clear. In this study, we report infrared photodissociation spectroscopy of H⁺(H₂O)₆·M_m (M = Ne, Ar, Kr, Xe, H₂, N₂, and CH₄) in the OH stretch region to investigate messenger(M)-dependent cluster structures of the H⁺(H₂O)₆ moiety. The H⁺(H₂O)₆, the protonated water hexamer, is the smallest system in which both the H₃O⁺ (Eigen) and H₅O₂⁺ (Zundel) hydrated proton motifs coexist. All the spectra show narrower band widths reflecting reduced internal energy (lower vibrational temperature) in comparison with bare H⁺(H₂O)₆. The Xe-, CH₄-, and N₂-mediated spectra show additional band features due to the relatively strong perturbation of the messenger. The observed band patterns in the Ar-, Kr-, Xe-, N₂-, and CH₄-mediated spectra are attributed mainly to the “Zundel” type isomer, which is more stable. On the other hand, the Ne- and H₂-mediated spectra are accounted for by a mixture of the “Eigen” and “Zundel” types, like that of bare H⁺(H₂O)₆. These results suggest that a messenger sometimes imposes unexpected isomer-selectivity even though it has been thought to be inert. Plausible origins of the isomer-selectivity are also discussed.