In this chapter, we report a possible alternative use of epigenetics by applying methylation-sensitive amplified fragment length polymorphisms (MS-AFLP) to saffron traceability. Saffron is the most expensive plant-derived product in the world and one of the most frequently adulterated. One of the most frequent adulteration is by adding to saffron stigmas different parts of the saffron flower itself to increase volumes. While DNA is the same in all the parts of the plant, the epigenetic state can vary according to the organ and/or tissue of origin, making it possible to discriminate the stigmas from the other parts of saffron flower. In the subsequent method, the protocol to carry out a MS-AFLP analysis of saffron DNA methylation patterns is described.