Unifloral honeys have a high commercial value and should undergo a strict quality control before marketing. This study aimed at determining floral origin, polyphenolic compounds and antioxidant activity in 7 samples marketed as lavender and thyme honeys. The samples were subjected to pollen analysis to confirm their botanical origin. Coupled chromatographic techniques (HPLC-DAD-ESI-MS) were optimized for the separation and identification of polyphenolic compounds. The antioxidant properties of the samples were determined by spectrophotometric methods. Pollen profile analysis revealed that only 3 out of 5 alleged lavender honeys contained a low percentage (0.6-1.5) of lavender pollen; and there were only traces (0.1-0.6%) of thyme pollen in the alleged thyme honeys. Polyphenolic constituents did not allow for the clear separation of honey samples, revealing no marker compounds previously associated with lavender and thyme honeys. All samples contained large amounts of chlorogenic acid, chrysin, hesperetin, kaempferol and p-coumaric acid; as well as abscisic acid, a plant hormone known to be present in floral nectar and honey. Our results suggest that only one of five alleged lavender honeys and neither of the two alleged thyme honeys are true unifloral honeys. However, they can still provide various health benefits, such as being good sources of antioxidants. There was no relationship between the antioxidant activity and the uni- or multifloral character of the honey samples. Total phenolic content and antioxidant activity was the lowest in the honey sample with lavender and the highest in one of the alleged lavender honeys. Our findings highlight the importance of microscopical and phytochemical analyses of honeys before marketing, to ensure satisfactory quality for customers.