Controversial arguments exist as to whether Nelumbo is native in Japan or introduced. We encountered considerable amounts of Nelumbo fossil pollen grains during the course of pollen analysis of the Karako Mire sediments, Japan. Pollen assemblages with a carbon-14 dating, and available stratigraphic data, indicate that the vegetation around the mire would have been an evergreen broad-leaved forest of Quercus, subgenera Cyclobalanopsis and Castanopsis, during the period 6000-2000 years B.P., and subsequently, for the last 2000 years, secondary Pinus forest. Nelumbo fossil pollen grains occur in more than half of samples studied, in notable amounts (7% or less). It is most likely that Nelumbo grew during a warm climate in a mire environment for more than 6000 years. These data are useful for the reconstruction of Nelumbo history in Japan.