A high performance liquid chromatography–diode array detection–tandem mass spectrometry (HPLC–DAD–MS/MS) method for determining the floral origin of chaste honey and rape honey samples was firstly presented in this study. Kaempferol, morin and ferulic acid were all used as floral markers to decipher chaste honey from rape honey. Chromatographic fingerprinting at 270 nm and 360 nm could be used as a way to characterise chaste honey and rape honey according to their unique profiles. Principal component analysis (PCA), partial least squares (PLS), partial least squares-discrimination analysis (PLS-DA) and soft independent modeling of class analogy (SIMCA) were applied to distinguish the honeys floral origins. The results displayed that both chaste honey and rape honey were able to be identified relative to their floral sources with these analytical methods. Therefore, the study is encouraging in promising the traceability of honey from unifloral to multifloral sources.