New Zealand ma̅nuka (Leptospermum scoparium) and kanuka (Kunzea ericoides) honeys contain a unique array of chemical markers useful for chemical fingerprinting. We investigated the presence of 13 potential marker compounds in nectars of the major honey crop species. We confirmed that leptosperin, lepteridine, 20-methoxyacetophenone, and 2-methoxybenzoic acid are exclusive to ma̅nuka nectar whereas lumichrome is unique to kanuka nectar. 3-Phenyllactic acid and 4-hydroxyphenyllactic acid are present in ma̅nuka and kanuka nectars. Leptosperin, lepteridine, 3-phenyllactic acid, and 4-hydroxyphenyllactic acid are chemically stable over prolonged storage, but not 2-methoxybenzoic acid and 20-methoxyacetophenone. Accordingly, leptosperin and lepteridine are definitive chemical markers for authentication of ma̅nuka honey. An optimal concentration cut-off was established for the floral source-specific markers: leptosperin (94 mg/kg), lepteridine (2.1 mg/kg), 20-methoxyacetophenone (2.0 mg/kg) for ma̅nuka honey, and lumichrome (4.5 mg/kg) for kanuka honey. The use of leptosperin and lepteridine as fluorescence markers for ma̅nuka honey authentication is reinforced.