This study investigated early to middle Miocene ostracods from the Yatsuo Group (ca. 17–15 Ma), located on the Japan Sea coast of central Japan. Ostracods from this area consist of 100 species in 60 genera, with two assemblages defined by Q-mode cluster analysis. The five most abundant genera of each assemblage are Krithe, Propontocypris?, Cytherella, Argilloecia, and Falsobuntonia in assemblage A, and Schizocythere, Cornucoquimba, Callistocythere, Neomonoceratina, and Paracytheridea in assemblage B. The depositional environment of each assemblage can be defined as (1) outer-shelf to bathyal areas (assemblage A) and (2) inner-shelf areas (assemblage B). Stratigraphic changes in the faunal composition, with changes in lithofacies, suggest a shallowing-upward phase in this sedimentary basin. These assemblages contain the same species or genera as corresponding Pacific faunas in the early to middle Miocene. The assemblage containing bathyal genera such as Cytherella and Krithe from Yatsuo at 17–16 Ma is the oldest record from the entire Japan Sea coast, and their fossil records are common to Cenozoic bathyal genera among the Pacific fauna. This fact indicates that these genera could migrate from the Pacific Ocean through the deep-sea passageway to the Japan Sea since at least around 17 Ma during the early Miocene. The shallow-water assemblage of the inner-shelf area around 15.7 Ma has only a small percentage of cold-water genera. The paleo-water temperature in the shallow-sea area around 15.7 Ma in Yatsuo would have been intermediate between warm (subtropical) and cold marine climates around 16 Ma in the Japanese Islands. The ostracod fauna from Yatsuo is significant for the paleogeography and faunal migration of benthos in the Northwest Pacific Ocean during the formation period of the Japan Sea caused by back-arc spreading.