The cocoa tree (Theobromacacao L.) is a tropical perennial plant belonging to the Sterculiaceae family. The cultivation of cocoa dates long before the arrival of the Spaniards in Central America. It is difficult to pinpoint the origin of the cocoa tree. However, the most probable hypothesis locates the cocoa tree in the Amazon basin [1] [2] [3] [4]. Three main genetic groups of cocoa named Criollo, Forastero and Trinitario have been established on the basis of their morphological characteristics and geographic origins [5] - [11]. Although Theobromacacao is native to America, nearly 70% of the world’s harvest is currently produced in West Africa. Cocoa beans are mainly used in the preparation of chocolate. Before being exported, cocoa beans undergo fermentation following a drying process. These two steps are generally conducted as traditional indigenous processes (Ho, Zhao & Fleet, 2014), the details of which depend on the country of origin, but which influence the taste and flavor of cocoa products. The characteristics of the geographical origin of fermented cocoa beans could thus be linked both to the fermentation and drying procedure and to the varieties of cocoa, giving a range of economic values to the product, hence the need for adequate methods. of traceability. The processed cocoa bean is composed mainly of triacylglycerides (cocoa butter, 45% - 54%) and protein (11.5%) and with sufficient levels of xanthine theobromine alkaloids (1.2% - 1.8%) and caffeine (0.25%) so that these are easily detected and quantified. The chemical composition of cocoa beans is related not only to the variety but also to the quality of fermentation and drying. Thus, most publications in the field of cocoa traceability have mainly focused on analyzing the chemical composition of processed cocoa beans (Crews, 2002; Oracz, Zyzelewicz, & Nebesny, 2013) by several methods, including infrared and NMR spectroscopy the chemical composition depends on the type of bean, the variety, the quality of fermentation and drying. Thus, most publications in the field of cocoa traceability have mainly focused on analyzing the chemical composition of processed cocoa beans (Crews, 2002; Oracz, Zyzelewicz, & Nebesny, 2013) by several methods, including infrared and NMR spectroscopy (Caligiani, Acquotti, Cirlini, & Palla, 2010; Caligiani, Palla, Acquotti, Marseglia and Palla, 2014), HPLC (Oracz et al., 2013) and mass spectrometry (Crews, 2002; Oracz and al., 2013). These different studies have shown that it is possible to differentiate the 3 varieties of cocoa (Forastero, Criollo and Trinitario) and to distinguish 3 cultivation zones in Côte d’Ivoire (Aboisso, Daloa and Divo), in particular on the basis of the caffeine and theobromine content. Recently, 1H NMR spectra of hydroalcoholic extracts from commercial cocoa beans have been used to characterize fermented cocoa beans according to variety and geographic origin (Caligiani et al., 2014), although a discrimination satisfactory was only possible after the complete assignment of the ¹H NMR spectra. In 2015, Diomande et al. used for the first time the Nitrogen and Carbon isotopic signature to characterize the geographic origin of cocoa bean of various origins. Although the results obtained were satisfactory, the measurement of the ¹⁸O/¹⁶O isotopic ratios had not been made. This work aims to characterize the origin of the cocoa bean from the isotopic ratios (in ¹⁸O/¹⁶O, in ¹⁵N/¹⁴N and ¹³C/¹²C) of theobromine taken as a probe molecule. A principal component analysis taking into account these three parameters makes it possible to highlight the characterization of the geographical origin. This same method will also be applied to caffeine with a view to the traceability of the various natural substances containing this molecule.