The authentication of food is an urgent concern owing to the increasing population and direct consequences of food on public health. Food authentication using DNA and omics‐based methods is gaining ground due to critical advantages notably in the areas of food adulteration in plant and animal‐based food and feed products and in determining the quality of food and food spoilage. Besides, there is greater demand for the detection of genetically modified foods (GMOs) and the detection of allergens, toxins, and carcinogens like tobacco in the food. The present review summarizes the advanced DNA and omics‐based methods (genomics, metabolomics, and proteomics) in the food industry. DNA‐based methods rely on specific markers known as reference genes for food authentication. Lactic acid bacteria such as Streptococcus thermophiles are being used as probiotics for treating infectious diseases and as an essential culture in the fermentation industry. Novel methods like CRISPR‐Cas have been recently introduced for the management of beneficial micro‐organisms relevant to food like probiotics and starter cultures by enhancing their production and restraining damaging pathogens. These methods can detect the source, presence of allergens, adulteration, and mislabeling in food products.