We describe the cypridoidean ostracod Heterocypris spadix sp. nov. from brackish water on Okinawa Island, Japan. The species closely resembles Heterocypris salina (Brady, 1868) but differs in that (1) the marginal infolds on valves are less developed, (2) the tubercles on the anterior margin of the right valve are completely covered by the selvage and invisible in inner view, and (3) the calcified inner lamella on the ventral margin of the left and right valves is scarcely evident in inner view, as the ventral margins of the valves bend inwardly. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA genes in H. spadix for future DNA barcoding and phylogenetic analyses. Our sample contained only females. A breeding experiment revealed that H. spadix females reproduce parthenogenetically. Another experiment showed that H. spadix has low tolerance to desiccation, with all individuals at 25°C dying between 1–2 hours after removal from water. We amplified and sequenced a partial 16S rRNA sequence for the endosymbiotic bacterium Cardinium from H. spadix. Infection by Cardinium may be related to the parthenogenetic reproductive mode we observed in H. spadix.