The class Monogenea (Platyhelminthes) is commonly parasitic on or in aquatic or amphibious vertebrates, mainly fishes, but rarely on aquatic invertebrates. In Japan, a total of 240 nominal species of monogeneans has so far been reported. Freshwater fishes are mainly parasitized by monopisthocotyleans. Based on the number of monogenean species collected by me from Japanese freshwater fishes, 600 to 900 species of freshwater monogeneans may be found on approximately 500 species of freshwater fishes. However, only about 80 monogenean species have been reported to date. And, in total, 15 alien monopisthocotylean species have been reported from alien freshwater fishes in Japan. Monogeneans can establish more readily together with their hosts than other groups of parasites because of their simple life cycle, and some of monogeneans, especially alien species, are known to cause negative impacts on wild and farmed fish stocks. The fauna of alien monogeneans in Japan should be urgently clarified. Only 12 species of monogeneans have been reported from six of the 90 endangered freshwater fish species. It is highly desirable to clarify the monogenean fauna of the freshwater fishes on the verge of co-extinction and to conserve biological diversity of monogenean species.