Concordia in Argentina and Salto in Uruguay are two neighbouring regions famous for the production of a precious citrus honey, whose valorisation passes through the ability to guarantee its geographical origin. In this study the influence of the different botanical origins (monofloral and polyfloral) within the same region of origin on the different stable isotope ratios was evaluated. Moreover, the effectiveness of the stable isotope ratio parameters δ13Choney, δ13Cprotein, δ15Nprotein, δ34Sprotein, δ2Hprotein and δ18Oprotein to discriminate between honeys produced in the internal border regions between Argentina and Uruguay (namely, Concordia and Salto) and honeys sampled in the two different Uruguayan coastal regions (Canelones and Maldonado) was tested on 82 monofloral and polyfloral honey samples. The results show that the different stable isotope ratios, except that of nitrogen, are not significantly influenced by the botanical origin of the samples. The sulphur isotopic ratio of proteins and carbon of honey are the most significant parameters for discriminating the geographical origin of the honeys considered. Applied a Principal Component Analysis, the first two factors overall explain 63.5% of the total variance, while the Discriminant Analysis provided optimal discrimination between the three origins, reaching a minimum of 96.7% correct reclassification.