Food fingerprinting approaches are expected to become a very potent tool in authentication processes aiming at a comprehensive characterization of complex food matrices. In this chapter, we provide a critical view on emerging molecular fingerprinting techniques, including elemental, foodomics, and microbial fingerprints. Among these, molecular biology approaches focusing on DNA‐based techniques are increasingly being evaluated for use in fingerprinting studies. Recent developments in DNA sequencing, particularly with respect to technical advances in the field of next generation sequencing, should greatly facilitate food authentication and enhance food authenticity in the future.