Three infraspecific taxa, var. japonica, var. hirsutiflora, and var. boniensis, were recognized in Angelica japonica by Yamazaki (1990). He considered that var. boninensis is distributed both in the Bonin and the Daito Islands. In this paper, in order to evaluate taxonomic status of var. boninensis, we examined the populations of the three varieties on the basis of allozyme analysis. In the obtained UPGMA dendrogram, three major clusters of the populations from the following three areas were recognized: I) the southern part of Kyushu, the Hedo population of Okinawa Island and the Daito Islands; II) the Bonin Islands; and III) Okinawa Island and the Yaeyama Islands. The plant populations of the Daito and the Bonin Islands, which were identified as var. boninensis by Yamazaki (1990), were divided into two different clusters based on the UPGMA dendrogram. The values of genetic identities among the three clusters were lower than the mean values of those among conspecific plant populations. Differences in leaflet shape coincided with these clusters. We concluded that the clusters I, II, and III can be taxonomically treated as independent species Angelica japonica A. Gray, A. boninensis Tuyama, and A. hirsutiflora Liu, Chao et Chung, respectively.