Quality parameters of different types of honey depends on several factors, such as bee species, pre and post-harvest management, environmental conditions and the botanical origin of the collected nectar. Thus, the geographical origin and honey species producing is mandatory to ensure its quality. This classification can be performed by determining its physicochemical parameters. Nonetheless, comparing all the attributes simultaneously is not an easy task. A feasible way to compare it can be reached by applying Principal Component Analysis (PCA) on its results, so, the whole physico-chemical analysis can be explored by once. In this study, different honey were evaluated and compared in order to distinguish about its origin and species. To do so, 14 samples of Jatai weyrauchi honey from Roraima and 15 samples of Jatai angustula honey from the State of Paraná were collected evaluated regarding on protein content, ash, pH, humidity, formaldehyde index, conductivity, acidity, reducing sugars, total reducing sugars, sucrose, soluble solids, hydroxymethylfurfural, viscosity, water activity and color. PCA required 7 PCs to explain 91.99% of the total variance, and it allowed for the sample classification according to its geographical origin and bee producing species. Only one sample (from Roraima) was erroneously classified as being from Paraná, while 3 Paraná samples were erroneously classified as being produced in Roraima. The analysis also shows that the samples classified as being from Paraná are similar regarding on the influence of protein, acidity, reducing sugars, total reducing sugars, viscosity, pH, color, conductivity, formaldehyde content and humidity, whereas Roraima samples are influenced by levels of hydroxymethylfurfural, water activity, sucrose and soluble solids. Thus, it is suggested that PCA can be applied to physico-chemical data for the classification of honey samples from different origins and producing species.