Lilium auratum var. platyphyllum has the largest corolla in genus Lilium and thus has been utilized as an important breeding material for oriental hybrid cultivars. L. auratum var. platyphyllum is endemic to the Izu archipelago located south of Tokyo. The wild habitat of this lily has diminished recentry, and the species is now listed as an endangered plant. We used a sequence-related amplified polymorphism (SRAP) markers approach to determine the genetic diversity of this species as a contribution to the conservation scheme. Fresh leaves of 65 individuals were collected from five islands (Izu-Oshima, Kouzu-shima, Miyake-jima, Mikura-jima, and Aoga-shima) to obtain DNA materials. We amplified 35 polymorphic bands using five combinations of SRAP primers. Multivariate analysis revealed the genetic diversity both among and within islands.