The morphology, allozyme variation and pollen viability in nine populations of Nuphar japonica, N. submersa, and unidentified intermediate plants were examined. A phenogram based on cluster analysis using 10 morphological characters revealed three cluster groups. Groups 1 and 3 had distinctive morphological characteristics and corresponded to the published descriptions of TV. japonica and N. submersa, respectively, whereas Group 2 showed intermediate values in most characteristics between the two species. In the allozyme study, many morphologically intermediate plants showed additive combinations of species-specific alleles in two loci (lapl and mdh3) from the two species. Pollen viability was significantly lower in intermediate plants than in the two species. Based on the evidence, we concluded that the intermediate plants were of hybrid origin between N. japonica and N. submersa and described them as N.×fluminalis.