Fraxinus chiisanensis Nakai, an endemic species to Korea and the related taxa from North America were analyzed to determine phenetic similarity and to make phylogenetic inferences. Eighty one specimens from sect. Fraxinus, subsect. Melioides [F. americana L., F. caroliniana Mill., F. pennsylvanica Marsh., F. profunda (Bush) Bush, F. velutina Torr, F. papillosa Lingelsh.] as well as F. chiisanensis were compared to evaluate the phenetic affinity using 22 morphological characters. The strong discontinuity existed between F. chiisanesis and other taxa of subsect. Melioides with respect to the shape of winter bud, the degree of leaf pubescence, and the number of leaflet serration. Foliar flavonoids were examined from subsection Melioides and F. chiisanensis. A total of 16 compounds was isolated and identified, mainly with flavonol and flavone. The analyzed flavonoid profiles were relatively uniform, and showed no distinct differentiation among taxa of subsect. Melioides except F. velutina. Comparing the result of Nuclear ribosomal DNA ITS and morphology, however, it was concluded that F. chiisanensis seems to be a highly primitive species within subsect. Melioides by traits unusual for this section : no petal and androdioecious flower with calyx. F. chiisanensis was probably differentiated from the ancestor group a long time ago and reflected no related extant species within this subsection.