The Japanese Islands is one of the important distribution areas and the diversity centers of the genus Angelica L. (Apiaceae), but previous research on the taxonomy and molecular systematics of Angelica seldom involved Japanese species. In this study, the fruits of 9 Angelica species (including 8 endemic species) from Japan were observed in morphology, anatomy and micro-morphology, respectively. It was revealed that (1) the result of observations using stereomicroscope: the fruit 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: most of 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) the classification key for those Japanese Angelica species, which was organized based on the above morphological characteristics and distinguishing features. Totally, the endemic Angelica species of Japan presented abundance of fruit features in morphology, probably providing strong evidence for their interspecies classification and relationships. Furthermore, this research, combined with the results of systematic studies on the Chinese Angelica genus, also proposed the potential phylogenetic position of Japanese endemic species and the relationships with their relatives in East Asian mainland.