The main objective of this research was to perform a preliminary chemical characterization of native cacao varieties from the "Theobroma cacao L." Germplasm Bank at INIA, in Loreto, Peru. To achieve this, bioactive compounds with antioxidant capacity such as catechin and epicatechin were quantified using high-performance liquid chromatography (HPLC) with a fluorescence detector, as well as methylxanthines (theobromine and caffeine). The fatty acid profile present in these varieties was also determined using gas chromatography. The results revealed significant variations in the chemical composition of the samples, highlighting that epicatechin was the predominant compound, followed by catechin. Additionally, notable variability in the concentration of fatty acids, especially palmitic and arachidonic acids, was identified, supporting the hypothesis of chemical differences among the samples...