Assessment of genetic diversity within and between populations is a prerequisite for sustainable utilization of domestic species. The domestic Muscovy duck (Cairina moschata) is an economically important species around the world for its unique meat taste and low-caloric content. It is one of the important domestic species in India as it ensures food security to the rural sectors. In this study, we have analyzed the genetic diversity and relationship of four Muscovy duck populations collected from different states (Assam, Mizoram, Odisha and Kerala) of India using mtDNA cytochrome b and nuclear DNA CYP2U1 genes. The results showed low genetic diversity among populations for both the genes. Kerala population showed significant genetic differences from the other three populations. The median joining network of cytochrome b gene suggested that the domestic Muscovy ducks present in India are the product of a single domestication event and probably introduced to India several years ago, as reported elsewhere. This study has also showed the suitability of nuclear DNA CYP2U1 gene in genetic diversity analysis.