Angelica L. acts as a significant representative of the family Apiaceae, of which the Japanese Islands is usually regarded as one of the important distribution areas and the diversity centers. In this study, we observed the fruits of 9 Angelica species (including 8 endemic species) from Japan in morphology, anatomy and micromorphology, respectively, in order to ascertain their taxonomical features and explore their potential relationships, and to provide more morphological evidence for taxonomical revisions and phylogenetic research. (1) The analyses of observations using stereomicroscope revealed that: the fruits usually obovate and oblong in shape, glabrous or a little pubescent on surface, dorsalcompressed variously, dorsal ribs filiform or narrowwinged, lateral ribs narrowor widewinged, vittae 1 in each furrow and 2-4 in commissure. (2) The result of SEM suggested that: most species had parallel filiform primary ornamentations and squamous, bunchy, cordlike, hummocky or unobvious secondary ornamentations, some contained coralloid or radicular background, and appendages were granular generally. (3) Based on the above morphological characteristics and distinguishing features, the classification key for those Japanese Angelica species was organized, and combined with the results of systematic studies on the Chinese Angelica, it was also proposed the potential phylogenetic position of Japanese endemic species and the relationships with their relatives in East Asian mainland. Totally, the endemic Angelica species of Japan presented abundance of fruit features in morphology, probably providing strong evidence for their interspecies classification and relationships.