Abstract: Foxtail millet (Setaria italica) is a cultivated nutritional cereal, which originated in South Asia and is considered one of the oldest cultivated millets in India. DNA fingerprinting is mandatory for registration of newly developed varieties with National Bureau of Plant Genetic Resources (NBPGR) and Protection of Plant Varieties and Farmers' Rights Authority (PPV&FRA). Due to the limited availability of genomic information in foxtail millet, the use of DNA based markers in fingerprinting of crop varieties is also limited. Hence in the present investigation, available RAPD and SSR markers of cereals are used for fingerprinting the foxtail millet varieties. The newly released variety ATL 1 is differentiated from popular variety CO (Te) 7 using SSR and RAPD markers. About 66 maize SSR primers, 16 sorghum SSR primers, and 10 RAPD primers were used in the study. Out of 66 maize SSR markers used for study, one showed polymorphism. The marker umc1704 showed polymorphism between CO (Te) 7 and ATL 1 by the presence of 670 bp allele CO (Te) 7. The RAPD primers OPB4, OPA5, OPA11 and OPB1 also helped for differentiation of the two varieties. The identified makers will help for genetic purity testing of CO (Te) 7 and ATL 1 in the seed chain.