Microorganisms are an essential component of all natural cheese varieties and play important roles during both cheese manufacture and ripening. They can be divided into two main groups; starters and secondary flora. The starter flora, Lactococcus lactis, Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii used either individually or in various combinations depending on the cheese variety, are responsible for acid development during cheese production. Starters may be either blends of defined strains or, as in the case of many cheeses manufactured by traditional methods, composed of undefined mixtures of strains which are either added at the beginning of manufacture or are naturally present in the cheese milk. During cheese ripening, the starter culture, along with the secondary flora promote a complex series of biochemical reactions which are vital for proper development of both flavour and texture. The secondary flora is composed of complex mixtures of bacteria, yeasts and moulds, and is generally specifically associated with particular cheese varieties. In many cheese varieties, the action of the secondary flora contributes significantly to the specific characteristics of that particular variety. The secondary flora may be added in the form of defined cultures, but in many situations is composed of adventitious microorganisms gaining access to the cheese either from ingredients or the environment. During cheese manufacture and ripening, complex interactions occur between individual components of the cheese flora. Environmental factors within the cheese also contribute to these interactions. Elucidation of such interactions would greatly add to our understanding of the cheese ripening process and would enable a more targeted approach to starter/adjunct selection for cheese quality improvement. In the past, research in this area was dependent on classical microbiological techniques, which are very time consuming, not suitable for handling large numbers of isolates and generally not suitable to studies at sub species levels. However, developments in this area have recently undergone a major revolution through the development of a range of molecular techniques, which enable rapid identification of individual isolates to species and strain level. Application of such techniques to the study of cheese microbiology should lead to major advances in understanding this complex microbial ecosystem and its impact on cheese ripening and quality in the coming years.