Manuka honey from New Zealand is often considered to be a medicinal product of special value due to its high level of antimicrobial activity. Therefore, the distinct authentication of its botanical origin is of great importance. Aside from the common pollen analysis, it is in this respect particularly the analysis of the phenolic acids, flavonoids, and norisoprenoids that is described as useful. In the present study, numerous manuka honeys were analyzed by UPLC-PDA-MS/MS after solid-phase extraction and compared to other kinds of honey to define marker substances characteristic for manuka honeys. The PDA profiles obtained differed markedly from each other so that the individual honey samples could be assigned to three groups. For the honeys of group 1 the comparably high concentrations of 4-hydroxybenzoic acid, dehydrovomifoliol, and benzoic acid proved to be typical, whereas the profiles of group 2 showed high kojic acid and 2-methoxybenzoic acid intensities. The manuka honeys of group 3, on the other hand, yielded high amounts of syringic acid, 4-methoxyphenyllactic acid, and methyl syringate. Furthermore, the comprehensive comparison of manuka honeys to other unifloral honeys revealed that especially kojic acid, 5-methyl-3-furancarboxylic acid, leptosin, unedone, 2-methoxybenzoic acid, 4-methoxyphenyllactic acid, 3-hydroxy-1-(2-methoxyphenyl)penta-1,4-dione, and methyl syringate were useful for distinguishing manuka honeys from the other kinds of investigated honeys. Moreover, kojic acid, unedone, 5-methyl-3-furancarboxylic acid, 3-hydroxy-1-(2-methoxyphenyl)penta-1,4-dione, and lumichrome were identified in manuka honey for the first time.