The quality of a DNA isolation method depends, among others, on the target tissue and the metabolites therein. Geoffroea decorticans Burkart (chañar) is a species that has nutritional andpharmacological potential. However, an effective method of DNA extraction capable of facilitating population studies and food genetic traceability has not been studied yet. The objective of thepresent work was to evaluate four methods of DNA extraction from leaves and chañar-based foods. The methods were evaluated based on yield, DNA purity, and molecular markers. The CCI-P (CTAB/ Chloroform-Isoamylalcohol/pellet) method showed the highest yield of DNA obtained from leaves. However, the CPCI-SC (CTAB/Phenol-Chloroform-Isoamylalcohol/silica-column) method was the only one that resulted in acceptable DNA quality with both parameters (A260/A280 and A260/A230). The leaf DNA obtained with this method showed a greater amount of fragments with RAPD, and an acceptable amount of fragments with ISSR. On the other hand, the CCI-P method showed a higher yield of DNA from arrope de chañar (syrup). However, the CPCI-SC method was the only one that had relatively better DNA quality, which allowed the amplification of molecular markers. Regarding chañar flour, the CPCI-SC method showed the highest yield, DNA quality and good amplification with molecular markers. Therefore, the CPCI-SC extraction method is efficient for obtaining DNA from different matrices, and can support studies for a possible designation of origin of chañar-based foods.