Indigenous lactic acid bacteria contribute to the taste and flavour of traditional dairy products. Therefore, the traditional dairy products might be an interesting reservoir of indigenous lactococcal strains responsible for development of the specific flavour compounds. Consequently, characterized indigenous isolates might be used as a starter culture. The development of molecular techniques provides a new perspective for characterization of the “new lactococcal” strains. However, there is no unique approach suggested for molecular characterization of the indigenous strains associated with the traditional products. The aim of this review is to provide an insight into varieties of experimental approaches applied for molecular characterization of indigenous lactococci associated with traditional dairy products.