Traditional cheeses contain a complex microbiota made up of deliberately added starter cultures and indigenous microbiota. Their development and expression under the pressure of cheese-making and ripening practices have a considerable influence on cheese quality and safety. In the context of cheeses bearing a geographical indication such as PDO and PGI cheeses, particularly those made from raw milk, the microbiota contributes to the typicality of the cheese. The balance between deliberately added cultures (lactic starters or protective cultures) and the indigenous microbiota is a major issue in “terroir” cheeses. High-throughput omics approaches have opened up new ways of characterising the diversity of milk and cheese microbiota. The presentation will share some recent knowledge about the microbiota of French PDO milk and cheeses, and their biogeography. It will also illustrate how systemic studies of the dairy food chain can help decipher the main sources of microbial diversity for cheese and their drivers among farming and cheese-making practices.