The principal phenolic compounds and methylglyoxal were analysed in New Zealand Leptospermum scoparium (manuka) and Kunzea ericoides (kanuka) honeys. These honeys shared six phenolic acids as primary components and differentiation was possible as relative proportions varied. Manuka honey contained an elevated concentration of a trimethoxybenzoic acid and methylglyoxal; and 2-methoxybenzoic acid and methylglyoxal concentrations were linearly correlated in fresh manuka honey. Kanuka honey contained an elevated concentration of methoxyphenyllactic acid. The concentration of the phenolic components increased with maturation in both honey types; and this profile development, along with a corresponding increase of methylglyoxal concentration, was linear in manuka honey. Nectar analysed from the plant species contained the same phenolic components as the honeys. These results demonstrated the phenolic profile could be used to differentiate the honey types, heat treatment of honey could be identified, and the presence of these components may contribute to the efficacy of these honeys in therapeutic uses.