Spicantopsis hancockii (Blechnaceae) was once thought to be endemic to Taiwan, and later known to occur in the Tokara Islands in southern Japan. Because of its high morphological similarity to S. niponica endemic to Japan, the identification of the Tokara Archipelago populations has been controversial. MIG-seq analysis using 2324 SNPs revealed that S. niponica and the samples of S. hancockii from Taiwan formed two distinct clusters, while the population of S. hancockii in the Tokara Islands was included in the cluster of S. niponica. Micromorphological traits of sporangia observed in the Tokara populations coincide with those of S. niponica reported by the previous study. Therefore, it is appropriate to treat the Tokara populations of “S. hancockii” as the southernmost range of S. niponica, not as S. hancockii. As a result, S. hancockii is resurrected as an endemic species to Taiwan.