We have measured the isomeric transition between the energetically lowest lying isomers of S6 and C2-symmetry of (CH3OH)6. The clusters are size-selected by deflection in collisions with He, and the isomers are identified by their infrared spectra of the OH-stretching vibration. The measurements are carried out at three source temperatures 253, 300 and 373 K which correspond to the cluster temperatures 93, 106 and 135 K. The latter ones are estimated by a relaxation model that accounts for the cluster formation and the energy released by the condensation. The transition takes place at a cluster temperature of about 102 K which is in agreement with the Molecular Dynamics simulation of such a transition at about 117 K using a realistic model potential.