Many Mule, Muscovy, and Bikini duck flocks in different duck-producing regions in Egypt have shown signs of a new disease designated "short beak and dwarfism syndrome" (SBDS) since 2015. The ducks with SBDS showed strong growth retardation with beak atrophy, enteritis, and paralysis. Although the mortality rate was 2%–8% in affected flocks, the morbidity rate was 20%–50% and even 80% in some regions. The disease is characterized by dyspraxia, weight loss, a protruding tongue, and high morbidity and low mortality rates. To characterize the etiological agent, a virus was isolated from the allantoic fluid following serial passage in embryonated duck eggs. This virus causes a cytopathic effect in duck embryo fibroblast (DEF) cells. Using enzyme-linked immunosorbent assay (ELISA), the isolate was positive for the antigen of goose parvovirus (GPV). The bovine sperm agglutination test indicated that the virus was most closely related to GPV strain. Together, these data indicated that the isolated virus from mule ducks with SBDS disease is a GPV-related parvovirus causing and that it is divergent from classical GPV isolates.