The thermally assisted hydrolysis and methylation (THM) reaction of hexuronic acids and xylobiose using tetramethylammonium hydroxide (TMAH) was studied. The results were compared to the THM of the corresponding matrix polymers. Glucuronic and galacturonic acids—which we take as model substances—produce unique products, namely 2,4,6-tri-O-methyl-3-deoxy-glucaric acid dimethyl ester and tri-O-methyl-3-deoxy-galactaric acid dimethyl ester, respectively, together with their epimers. The EI mass spectrum, as well as a proposed fragmentation pathway, are presented. These markers, however, are not detectable in the THM of the corresponding polymers, i.e. the hemicellulose xylan and pectin.