Marker is a tag which is either scorable or apparent for identification of an individual of traits associated with an individual. A molecular marker is the change in nucleic acid sequence or conformation which can be utilized for identification or classification of an individual. Molecular markers directly reveal the polymorphism at the level of DNA. These are tags that can be used to identify specific genes and locate them in relation to other genes. The use of molecular markers is indispensable for the establishment of core collections and characterization of garlic accessions. Molecular markers such as DNA fingerprinting and AFLPs have been used to detect duplicated accessions in Garlic collections. Moreover, molecular markers have been used for detection of somaclonal variants generated by in vitro culture of garlic, for determination of fertile clones in garlic, disease resistance and clones producing S-amino acids. In order to link more quality traits in garlic we need to develop more versatile markers in this crop which will be further utilized for gene mapping and gene transfer technology.