We describe the ostracod Lissostrandesia fonticola gen. et sp. nov. in the subfamily Cypricercinae McKenzie, 1971, collected from six rheocrenic springs in Japan. The populations sampled were separated by up to 1000 km, and some of them by one or two marine straits, which comprise significant barriers for freshwater animals. Lissostrandesia differs from the other 13 cypricercine genera in (1) lacking a groove and inner list on the anterior inner margin of the left valve; (2) having b and d setae on the fifth limb; (3) having d1 and d2 setae on the sixth limb; (4) having a stout attachment of the caudal ramus; (5) having a Triebel's loop on the dorsal branch of the attachment; and (6) having a long free ventral branch, its length more than twice its width, and (7) having a free dorsal branch contributing to a tip on Triebel's loop. These differences were enough to warrant establishment of a new tribe, Lissostrandesiini, to accommodate the new genus. We present a key to the genera in Cypricercinae. The maximum p-distance for the mitochondrial cytochrome c oxidase subunit I (COI) gene among six local populations was 0.662%, a low value indicative of conspecificity. In addition, four populations with sample sizes of 13-21 individuals shared two main COI haplotypes, indicating high apparent connectivity. A trend of decreasing genetic diversity from south to north suggests L. fonticola has had a longer history on Honshu Island and dispersed northward from there. Using the 16S rRNA gene as a marker, we detected the endosymbiotic bacterium Cardinium, a group of "reproduction-manipulating" bacteria, in five populations, suggesting that L. fonticola is parthenogenetic. Passive dispersal is the most likely explanation for the broad distribution of this species across strong geographic barriers.