The botanical origin of honey determines its composition and hence properties and product quality. As a highly valued food product worldwide, assurance of the authenticity of honey is required to prevent potential fraud. In this work, the characterisation of Spanish honeys from 11 different botanical origins was carried out by headspace gas chromatography coupled with mass spectrometry (HS-GC-MS). A total of 27 volatile compounds were monitored, including aldehydes, alcohols, ketones, carboxylic acids, esters and monoterpenes. Samples were grouped into five categories of botanical origins: rosemary, orange blossom, albaida, thousand flower and “others” (the remaining origins studied, due to the limitation of samples available). Method validation was performed based on linearity and limits of detection and quantification, allowing the quantification of 21 compounds in the different honeys studied. Furthermore, an orthogonal partial least squares-discriminant analysis (OPLS-DA) chemometric model allowed the classification of honey into the five established categories, achieving a 100% and 91.67% classification and validation success rate, respectively. The application of the proposed methodology was tested by analysing 16 honey samples of unknown floral origin, classifying 4 as orange blossom, 4 as thousand flower and 8 as belonging to other botanical origins.