Genetic variation in an endangered tree species, Chionanthus retusus, was examined using enzyme electrophoresis. This species occurs in East Asia from Japan to Taiwan and southern China. In Japan, however, it occurs only in two restricted areas: at the northernmost tip of Tsushima Island between Japan and Korea, and in the eastern Gifu Prefecture (Tono region) of central Honshu. In the Tono region, the habitat of C. retusus is becoming fragmented under the influence of human activity and each stand contains a few individuals of C. retusus, while the population on Tsushima consists of approximately 1000 individuals. From the fossil evidence, C. retusus has been distributed continuously including the both two regions, and the present distribution is apparently relic in Japan. In contrast to the Tono population, the population of Tsushima seems to be stable. Comparing the genetic diversity and differentiation of the populations between these two regions should shed light on how a relic woody long-lived plant keeps and/or looses its genetic diversity, and how a population differentiates from other disjunct populations. Allozyme electrophoresis of 18 loci for the Tono region indicated that 22.2% of the loci are polymorphic (P) with a gene diversity of (h) 0.087. The population of Tsushima has 38.9% polymorphic loci and a gene diversity of 0.149. We could not find any spatial genetic structure of C. retusus in the Tono region by spatial autocorrelation analysis. These results suggest that considerable genetic variation is still present in the Tono region and the influence of the recent habitat fragmentation seems not so large, yet. Because C. retusus is a long-lived tree, the population history may hinder the effect of the fragmentation at present. The genetic diversity (G(ST)) between the populations of the Tono and Tsushima is 0.280, showing the genetic differentiation between these two regions has occurred.