Lilium japonicum Thunb. which has pink or white-colored funnel-like flowers, is distributed in Kyushu, Shikoku, and the western part of Honshu, the main island of Japan. L. auratum Lindl. which has large white flowers with yellow central stripes and red spots, is distributed in the eastern part of Honshu. Natural hybridization of these two species has only been found on the Izu Peninsula of Honshu. However, details of the variation and hybridity of the interspecific hybrid population of these species on this peninsula remain unknown. In the present study, we conducted a morphological examination using 43, 21, and 90 individuals of L. japonicum, L. auratum, and the putative hybrid, respectively, from six, four, and ten populations of the Izu Peninsula, respectively. In addition, we performed simple sequence repeat (SSR) analysis using 47, 41, and 106 individuals of L. japonicum, L. auratum, and the putative hybrid, respectively, from six, four, and ten populations, respectively. Putative hybrid populations that resembled L. japonicum in morphology and SSR profile were found in the southern to eastern part of the peninsula, whereas those that resembled L. auratum and those exhibiting an intermediate morphology and SSR profile were found in the southern part of the peninsula. Large morphological variations exist in putative hybrid in the southern population, and interspecific hybridization has occurred in the southern and eastern populations. These results suggest that the center of natural hybridization is located in the southern part of the Izu Peninsula.