We describe the cypridoidean ostracod Cavernocypris hokkaiensis sp. nov. from riverbed sediments in an alpine stream at an elevation of ca. 1850 m in the Taisetsu Mountains, Hokkaido, Japan. This species differs from congeners in having (1) the outer surface of the carapace smooth, with sparse, tiny setae, but without shallow pits; (2) the carapace elongate rather than triangular in lateral view; (3) the antennula consisting of seven podomeres; (4) first palpal podomere of maxillula with five dorsodistal and one ventro-subdistal setae; (5) the fifth limb lacking setae b and d; and (6) the fifth limb lacking a vibratory plate. We provided the key to the Cavernocypris species. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA (18S) genes in C. hokkaiensis. Our sample contained only females, and we obtained a partial 16S rRNA sequence for the endosymbiotic bacterium Cardinium from C. hokkaiensis, indicating the possibility that this ostracod species reproduces parthenogenetically. Our field survey and observations of captive individuals suggested that C. hokkaiensis may be endemic to the Taisetsu Mountains, with a low population density, narrow distributional range, and slow maturation to sexual maturity.