Potamogeton×inbaensis Kadono is a natural hybrid between P. malaianus and P. dentatus. Oitoike pond, Pref. Fukuoka, is the only natural habitat of two endangered species, P. dentatus and P.×inbaensis, in Japan, but their population has been decreasing in recent years. We examined the direction of the hybridization and morphological characters in existent samples growing in Oitoike pond and herbarium specimens collected in the past. Potamogeton×inbaensis consisted of two types based on typification of the nuclear gene adh and the chloroplast gene rbcL: the hybrids of P. dentatus mothers (D-type) and those of P. malaianus mothers (M-type). Both types were roughly distinguishable by the leaf morphology. All existent P.×inbaensis in Oitoike pond was the M-type, but only the D-type was collected in the past. In drought experiments, P. dentatus exhibited lower survival than P. malaianus and M-hybrid. The habitat degradation such as increasing turbidity and a drought may cause the selective disappearance of the D-hybrids.