In the current work, we focus on the application of principal component analysis (PCA) to differentiate the floral origin of three types of honeys of the Yucatan Peninsula, Mexico [Tahonal (Viguiera dentata Blake, var. heliantoides), Dzidzilche (Gymnopodium floribundum Rolfen) and Haabin (Piscidia piscipula L.)], by using the volatile compounds of the honey obtained by HS-SPME/GCMS with PDMS/DVB fibres. About 70 peaks were detected in each honey sample, many of them were found with similar retention times in the analysed honeys. The PCA with three factors (nearly 68% of the total variance) discriminates between the three types of honeys, which leads us to conclude that it is possible to successfully differentiate samples from different unifloral honeys according to their volatile composition.