The cheese making process involves the growth and expressions of a large diversity of species. It starts by the growth of lactic acid bacteria in the curd before or during the curd drainage and it is followed by ripening steps which will determine the cheese properties. In large cheeses, if a phase of ripening is made at high temperature (e.g. 23°C), the development of Propionibacterium sp. generates propionic acid and CO2. These species are responsible of the eyes in Emmental. The development of Penicillium camemberti at the cheese surface of soft cheeses will produce the white coverage. If the rind is washed, the moulds cannot grow but the growth of yeasts and corynebacteria will produce cheeses rich in sulfur flavours and with an orange rind (wash rind cheeses). The use of molecular methods permits the description of the microbial ecosystem which appears now more complex than 15 years ago but it is still difficult to understand the interactions between the different species and the curd and also of the interactions between the species at the cheese surface. This emerging knowledge will definitely help to control the sensory properties of the cheese produced. This chapter is proposing to light up how the milk and the cheese technology select families of fungi and bacteria that will give the cheese diversity.