Presently, more than 40 species of the genus Milnesium Doyère, 1840 (Tardigrada: Eutardigrada: Apochela: Milnesiidae) have been described. In Japan, however, almost all records of milnesiid tardigrades should be re-examined with the current criteria on the taxonomy of this genus, except for one species, the recently described Milnesium inceptum Morek, Suzuki, Schill, Georgiev, Yankova, Marley, and Michalczyk, 2019. In this study, we found two species, Milnesium pacificum sp. nov. and Milnesium tardigradum Doyère, 1840, from three southern islands and two cold regions in Japan, respectively. Milnesium pacificum sp. nov., having dorsal sculpturing, exhibits an early positive change in claw configuration. On the other hand, M. tardigradum s.s. from Japan has an early negative claw configuration change, as has been reported in a recent study on the neotype population of this species. We performed DNA barcoding for both species, which indicated that M. pacificum sp. nov. has a close affinity with an undescribed Milnesium species collected from Brazil, and that M. tardigradum from Japan represents the recently described subclade that contains specimens from Poland, Hungary, and Russia. The chromosome numbers were 2n = 14 in M. pacificum sp. nov. and 2n = 10 in M. tardigradum. We detected at least three species of the genus Milnesium present in Japan. Our results advance the investigation of the relationship between phylogenetic position and characteristic morphology as well as expand the known geographic range of M. tardigradum.