The Muscovy duck, Cairina moschata, is one of the native New World fowl domesticates. Nowadays, the domestic Muscovy ducks are worldwide distributed. They are bred for meat, feathers, eggs, and pets and even sometimes as guard animals. With the purpose of exploring genetic diversity and assisting molecular breeding of this valuable waterfowl species, we propose to sequence the genome of Muscovy duck. We employ the 10X Genomics strategy to sequence and assemble a male domestic Muscovy duck genome. We generate 133.5 Gb clean data. The assembled genome is about 1.1 Gb. The contig N50 and scaffold N50 are 80.71 kb and 4.38 Mb, respectively. A total of 15 transcriptomes from different organs/tissues are used for annotation. We report the first de novo genome sequence of the domestic Muscovy duck. It provides a valuable resource for future investigation of domestication history and genetics of Muscovy duck.