Honey color and other physicochemical characteristics depend mainly on the botanical and geographical origin. The study of these properties could make easier a correct classification of unifloral honey. This work determined the palynological characteristics and some physicochemical properties such as pH, electrical conductivity, and color (Pfund scale and the CIELa*b* coordinates), as well as the total content of the bioactive compounds phenols and flavonoids of ninety-three honey samples. Samples were classified as chestnut, blackberry, heather, eucalyptus, and honeydew honey. The study showed a close relationship between the physicochemical variables and the botanical origin. The five types of honey presented different physicochemical properties among them. A principal component analysis showed that Hue, lightness, b*, and Chroma variables were important for the honey types classification, followed by Erica pollen, pH, Cytisus, and Castanea variables. A forward stepwise regression analysis was performed introducing as dependent variables the color (mm Pfund) and the Chroma and the Hue variables. The regression models obtained explained 86%, 74%, and 86% of the variance of the data, respectively. The combination of the chromatic and physicochemical and pollen variables through the use of multivariable methods was optimal to characterize and group the honey samples studied.