Monachosorum arakii Tagawa is a plant species endemic to the western part of the main island of Japan. It is characterized by large bulbils on the rachises and is a close relative of M. henryi Christ, which can be found in the Sino-Himalayan region and is not present in Japan. Although M. arakii was reported to be a hexaploid, we determined that it is a pentaploid based on chromosome counts. All of the herbarium specimens examined, including the holotype, had irregularly shaped spores, suggesting that this is a sterile hybrid species. Analysis of the nuclear gapCp sequences also supported its hybrid origin from M. henryi (tetraploid) and M. nipponicum Makino (hexaploid). It should be noted that the parental species of M. arakii, which are endemic to Japan, only co-occur in China. It is possible that the hybrids are relicts from the time when M. henryi were also present in Japan, and are now reproducing only vegetatively by rhizome division and bulbil production. The updated taxonomic treatments for Monachosorum species provided in the current study recognize four species and two hybrid taxa.