Dihydroxyacetone (DHA) and methylglyoxal (MGO) are unique carbohydrate metabolites of manuka honey. A method for the reliable quantification of DHA in honey samples was established, based on derivatization with o-phenylenediamine (OPD) and subsequent RP-HPLC with UV detection. The previously unknown reaction product of DHA and OPD was identified as 2-hydroxymethylquinoxaline by spectroscopic means. DHA was exclusively determined in 6 fresh manuka honeys originating directly from the beehive as well as 18 commercial manuka honey samples, ranging from 600 to 2700 mg/kg and 130 to 1600 mg/kg, respectively. The corresponding MGO contents varied from 50 to 250 mg/kg in fresh and 70 to 700 mg/kg in commercial manuka honey samples. A good linear correlation between DHA and MGO values in commercial manuka honeys was observed, resulting in a mean ratio of DHA to MGO of 2:1. In contrast to this, the DHA-to-MGO relation was much higher in fresh manuka honeys but approximated to a ratio of 2:1 while honey ripening. Heating experiments revealed that MGO formation based on thermal treatment as a consequence, for example, of caramelization in honey does not occur. DHA and MGO can serve as suitable unique quality parameter for manuka honey.