A new species Hymenaphorura yoshii sp. nov. from Myoujindo Cave in Japan is described and illustrated. The new species is the most similar to H. mystica Pomorski, 2001 and H. palaearctica Pomorski, 2001 but can be distinguished from former species by the build of postantennal organ, the clearly differentiated into macro- and microsetae chaetotaxy and the large and curved anal spines while the H. palaearctica differs from the new species by the absence of pseudocellus on thoracic tergum I, the presence of 4 macrosetae on abdominal tergum V and 2 lateral teeth on claw. The key to the world species of Hymenaphorura is also provided.