Three medicinal species of the genus Polygala were examined by comparative morphology, anatomy and TLC analysis. They were classified into three species, and distinctly divided into two groups in this study. Group I is composed of P. japonica, P. sibirica and Group II P. tenuifolia. Considered on the relationships between two groups by the differences of leaf shape, adnated part of petal, flower colour, fruit shape etc., Group II may have been independently evolved from the common ancestor by having one raw of palisadelike chlorenchyma under the stem epidermis through the different pathway. It is also suggested that the taxa of Group II appear to be more advanced than those of Group I.