Coniothyrione is a xanthone‐derived antibiotic reported several years ago by researchers at Merck & Co. Inc. Revision of the position of the chloro substitution was recently proposed on the basis of empirical reinterpretation of the carbon chemical shift data and a hypothetical biosynthetic argument without the acquisition of any new spectral data to support the postulated change in substituent location. The originally published HMBC data lead to an equivocal assignment of the structure and do not provide a solid basis of support for either structure. Neural network 13C chemical shift calculations and density functional theory calculations also led to undifferentiated structures. Definitive confirmation of the structure of coniothyrione based on the acquisition and interpretation of 1,1‐ADEQUATE and inverted 1JCC 1,n‐ADEQUATE data is now reported. Copyright © 2013 John Wiley & Sons, Ltd. Advanced microscale 2D NMR techniques have been utilized to unequivocally confirm the recent suggested revision of the structure of coniothyrione on the basis of chemical shift calculations and a biogenetic argument. The structure has been rigorously confirmed as the 4‐chloro xanthone using 1,1‐ADEQUATE and high level density functional theory calculations of 13C chemical shifts as well as nJCH and nJCC (n = 1–3) coupling constants. There is excellent agreement between the calculated and measured parameters for the 4‐chloro xanthone.