The historical reconstruction of the origin and dispersal of plant taxa in space and time facilitates a better understanding of their modern distribution patterns. However, most studies of paleobiogeography have focused on terrestrial plants, and the distribution changes of aquatic plants are less well understood. Here we study the lotus plant Nelumbo (Nelumbonaceae), an aquatic perennial herb, with a disjunctive distribution across East, South and Southeast Asia-North Australia and North America. The reproductive organs ofNelumbo changchangensis He et Jin from the Eocene of Hainan, China are supplementarily described. Analysis of the spatial and temporal distributions of Nelumbo in the geologic past indicates that the genus first occurs in mid-latitude area of Laurasia in the Early Cretaceous, then becomes widespread in North America and Eurasia and expands into South America during the Late Cretaceous, and reaches its maximum northern limit during the Eocene. The genus persists and thrives in North America and Eurasia until the Pliocene. The Pleistocene ice age causes the extinction of Nelumbo in Europe and central Asia, and its populations in North American and Asia are also restricted to refuges of lower latitude. Like the terrestrial plants Metasequoia (Cupressaceae) and Nordenskioeldia (Trochodendraceae), the fluctuations of Nelumbodistribution ranges are also linked to climatic changes in the Cenozoic. The cooling climate and increasing seasonality in the Eocene of East Asia may favor the origin of tubers and the differentiating of the ecotypes in lotus, which allow the deciduous type to survive in cold winters.