This Zenodo archive contains the spectroscopy data for the analysis of deuterated cyclohexene compounds. The data set supports the manuscript: "Molecular Rotational Resonance Spectroscopy-Informed Optimization of the Synthesis of Deuterated Isotopomers and Isotopologues of Cyclohexene" Justin T. Weatherford-Pratt, Jacob A. Smith, Martin S. Holdren, Haley N. Scolati, Reilly E. Sonstrom, Megan N. Ericson, Sarah E. Brewster, Diane A. Dickie, Brooks H. Pate, and W. Dean Harman This work is an extension of a previous study: Smith, J.A., Wilson, K.B., Sonstrom, R.E. et al."Preparation of cyclohexene isotopologues and stereoisotopomers from benzene." Nature 581, 288?293 (2020). https://doi.org/10.1038/s41586-020-2268-y The previous study contains additional spectroscopy results that can be found in the supporting information for the publication. That material is not replicated here. An in-depth description of the rotational spectroscopy analysis performed in the new manuscript can be found in the supporting information of that submission.