The identification of three light-coloured unifloral honeys was accomplished in this work. Chromatographic fingerprints were obtained through high performance liquid chromatography-electrochemical detection (HPLC-ECD). From the established chromatographic fingerprints, 17 common peaks with relatively high responses were selected as variables for classification. All 40 honey samples (including linden, Vicia villosa Roth and rape honeys) were correctly classified according to their botanical origin using a chemometric method. Additionally, several physicochemical parameters and the content of phenolic acids in the samples were determined. Using physicochemical parameters and phenolic profiles as variables, the overall correct classification rate reached 97.5% and 100%, respectively. The results indicated that the information obtained from the chromatographic ECD fingerprints was useful for the identification of the floral origin of the three light-coloured honeys.