The description of the rotational spectrum of a single molecular eigenstate in an energy region where conformational isomerization can occur is presented. The conformational isomerization rate can be determined from an analysis of the overall line shape of the spectrum. The isomerization dynamics are investigated through a time-domain analysis. It is shown that the nonstationary state produced by coherent microwave excitation has a well-defined conformational structure. However, the individual molecular eigenstates are a mixture of rovibrational states associated with the two conformations. The structural localization decays to the eigenstate equilibrium value at a rate defined as the isomerization rate. It is also shown that the line shape of the spectrum coalesces as the isomerization rate exceeds the difference between the characteristic rotational frequencies of the two conformers. The line shape profile of the eigenstate-resolved spectrum is well described by the Bloch equations modified for chemical exchange.