This study was conducted to elucidate the taxonomic characters of species of Korean Agrimonia by external morphological, microstructural(SEM) and anatomical analysis. The ranges of variations among species were also measured using characters. This study demonstrated that Agrimonia consists of three species; A. pilosa, A, coreana, A. nipponica. Shapes of leaflet and stipule, size of flower, number of stamens and size of fruit were morphological diagnostic characters to identify species. It was observed that papilla trichomes were distributed at the epidermis cells. In addition, polygonal crystals were observed on the surfaces of epidermal cells of A. coreana. The results of anatomical study indicated that mesophyll development were differential, and the star -shaped or granular crystals were observed on the tissue of leaves, stems and lateral root of three species in common. The three taxa were clearly classified by the results of the morphological and the anatomical characters. A new key to species was provided based on essential diagnostic characters.