Indigenous ducks play a vital role in sustainable livelihood of the poor duck farmers. In Tamil Nadu, two popular indigenous duck varieties viz., Sanyasi and Keeri are being reared traditionally by the duck farmers under nomadic system. In the same way, Kuttanad ducks are popular in Kerala and Assam ducks are popular in Assam. The present research work was undertaken to study the genetic distance between and within the indigenous ducks and exotic duck breeds by using duck specific microsatellite markers. From the blood samples the genomic DNA was isolated and characterized genetically. With the molecular data, dendrogram was constructed. This revealed that, Keeri, Sanyasi, Kuttanad and Assam ducks formed the first group with White Pekin in the second group and Muscovy in the third cluster. Among the Indian duck varieties, Keeri and Sanyasi ducks of Tamil Nadu were found to be closer to each other as indicated by the genetic distance value of 0.11. However, within this group, 26.33 and 29.87 per cent of differentiation were noticed between Assam and Sanyasi and Assam and Keeri ducks respectively. Higher genetic distance value of 0.92 (92 per cent) was observed between two exotic ducks. Based on the genetic distance and genetic diversity between the indigenous ducks, the duck varieties of Tamil Nadu, Kerala and Assam may be classified as distinct breeds.