Lactococcus lactis is one of the most important starter cultures in the dairy industry for the manufacture of a variety of fermented probiotic dairy products. Presently, four subspecies of L. lactis have been recognized, i.e. L. lactis ssp. cremoris, ssp. hordniae, ssp. lactis (including biovar diacetylactis) and ssp. tructae. Amongst them, the two subspecies lactis and cremoris are industrially important. Development of new strains of these two subspecies as starter culture with distinct characteristics generally requires the identification up to sub-species level. Classical identification methods such as physiological and biochemical tests can not differentiate organisms at species and subspecies levels. Moreover, these traditional phenotype-based methods encounter many challenges and shortcomings which limit their applicability. New approaches such as molecular characterization have been developed in the recent past. The molecular techniques provide a new perspective for characterization of the “new lactococcal” strains. However, there is no unique approach suggested for molecular characterization of the indigenous strains. Continuous research is going on around the world to improve the methodology and applicability of these methods as well as to make them economic in use. The objective of this review is to provide an insight into all genotypic approaches for the identification of L. lactis.