The purpose of this work was to develop a PCR method for the identification of Cynara cardunculus used in the elaboration of “Torta del Casar” cheese. One hundred five specimens were collected from different parts of the Extremadura region (Spain). Morphological characterisation was performed in situ at the time of sampling. Comparison of the morphological data was by genotypic characterisation. Different genetic profiles were obtained using seven random primers with the random amplified polymorphic DNA (RAPD) technique obtaining better results with the primer OPAE10. For the simple sequence repeat (SSR) technique, ten microsatellites were used, the best genetic profiles being obtained with the microsatellite CMAFLP-24. All the specimens were analysed with both primers, showing that the method provided a fast and accurate characterisation of C. cardunculus that could be used for the Protected Designation of Origin “Torta del Casar” as a tool for traceability and control in the process of elaboration of the cheese. Thistles with different genetic profiles were used in cheese-making finding that this is a good tool to monitorisation for quality control of cheese texture characteristics elaborated with these rennets.