Lilium longiflorum is endemic to the islands of the Ryukyu Archipelago in Japan and to the eastern seacoasts and satellite islands of the mainland of Taiwan. The species is an important ornamental plant, and is cultivated throughout the world. Lilium longiflorum has long been regarded as a self-incompatible species but the existence of selfing in some natural populations was suggested by isozyme analysis in a previous study. To confirm the occurrence of self-compatible individuals and to clarify the evolutionary shift of floral traits associated with degree of self-compatibility in L. longiflorum by comparative analysis, we used 17 populations of L. longiflorum, and two populations of L. formosanum, the genetically closest species of L. longiflorum, covering the entire species distribution. Artificial self-pollination revealed that not all L. longiflorum individuals are self-incompatible and there is substantial quantitative variation of self-incompatibility among L. longiflorum individuals and populations. Self-compatible dominant populations allopatrically and independently evolved at the periphery of the species distribution area, the northern Ryukyu Archipelago and Taiwan. Increasing degree of selfcompatibility in L. longiflorum correlated with reduced corolla length, corolla width, corolla volume, and anther length for the Ryukyu Archipelago, in contrast to only reduced corolla width and volume for Taiwan. Approach between anther and stigma was not observed in any populations. Our data indicate that in the Ryukyu Archipelago increasing degree of self-compatibility evolved floral traits related to mating system evolution, to selfing, that does not depend on adjacency between anther and stigma position, but not in Taiwan.