Global food security is recognized as one of the most important issues of the 21st century and takes many forms, including sustainable production, equitable distribution and reducing food waste. Within this overarching framework, defending the food supply from various threats requires a variety of tools. One of the most promising includes genomics, which is seeing diverse applications in crop improvements (e.g. increased crop yield, drought tolerance and pest resistance) but also has a central role to play in the surveillance of pathogens and the detection of food fraud. This talk will discuss the emergence of biodiversity genomics and its broad application in agricultural biomonitoring, as well as specific applications aimed to detect the adulteration and mislabelling of food ingredients an natural health products. Case studies will be discussed that demonstrate the relevance of various genomic tools as countermeasures against food fraud and their overall importance to food security.