A goose parvovirus (GPV) Y strain was isolated from Muscovy ducks in Anhui Province of China. By polymerase chain reaction method, its complete genomic sequence was found to be 5,106 bp in length, consisting of 444-bp inverted terminal repeat, 1,844-bp non-structural protein and 2,199-bp capsid protein (VP) regions. Then its sequence was aligned with the sequences of GPV and Muscovy duck parvovirus published in the GenBank using the neighbor-joining method. The phylogenetic analyses based on the VP3 gene sequences revealed that the GPV Y strain along with those from Taiwan belonged to the subgroup IIb, while other GPV strains from Muscovy ducks belonged to the subgroup Ib and most of other GPV strains isolated in China mainland were clustered in the subgroup IIa. The absence of the deduced 703-705NRT glycosylation site in VP region may explain the host specificity of the GPV Y strain. The complete genomic sequence of the GPV Y strain from Muscovy ducks will help to understand the molecular and evolutionary characteristics of GPV.