The correlation between the depth-areal distribution of the ostracod fauna in surface sediments and water mass properties in the open sea area of the southwestern-northeastern Japan Sea is presented. This is the first report of the temperature and salinity ranges for the ostracod fauna in this sea giving specific values for summer and winter. The fauna on the shelf and continental slope was divided into four assemblage types based on species composition. The depth distribution of these assemblages is stratified and differs between the northern and southern areas. The four assemblages are distributed according to the four different water masses; Tsushima Warm Current Surface Water (TWS), Tsushima Warm Current Core Water (TWC), Japan Sea Intermediate-Proper Water (JSI-P) and Japan Sea Central Water (JSC). Each assemblage is characterized by the following species and temperature-salinity range; (1) TWSA: Aurila spinifera, Schizocythere kishinouyei, 15–25°C and 33–34.5‰, (2) TWCA: Bradleya spp., Acanthocythereis munechikai, 7–20°C and 34–34.5‰, (3) JSI-PA: Krithe sawanensis, Acanthocythereis dunelmensis, 0–10°C and around 34‰, and (4) JSCA: Laperousecythere robusta, 5–15°C and around 34‰. The JSCA consists of a part of the species in the cryophilic Omma-Manganji ostracod fauna, which flourished during glacial periods in the Japan Sea. These species inhabit the characteristic and intercalated water mass between the shallowest-warmest current water (TWS) and deepest-coldest water (JSI-P). Their southern distributional areas have decreased since the Pleistocene due to the warm current flowing during interglacial periods. These species live in the restricted water mass environment, changing their depth distributions between the south and north of the Tsugaru Strait. They are interpreted to be the survivors of the cyclic environmental fluctuations in the Japan Sea during the glacial-interglacial periods since the Pleistocene. The results may indicate a water mass temperature of 5–15°C during glacial periods in the shallow-open areas in the Japan Sea.