Quality and safety control is a main topic for assuring food integrity that involves administration, industry and consumers. Analytical methods are essential to provide the required control, and molecular biology tools have become the key to address most of the related current issues throughout the whole food chain: authenticity, quality labels, safety and brand protection. The main advantages of molecular techniques for food safety and quality are the possibility to take strategic decisions just in time and the potential to adapt these methodologies to emerging needs with the same equipment and tools. Nowadays, these types of methodology are also easy to implement, offer robust results at a low time cost, provide solutions for very different types of analytical requirements, and exhibit in most cases the best cost/benefit ratio. International standards are commonly adopted by laboratories to guarantee their results. Molecular methods are increasingly being incorporated in accredited laboratories and are essential for a complete range of analytical methods.