The early Pleistocene ostracod fauna from the Hamada Formation (ca. 1.5–1.2 Ma) was investigated in the Shimokita Peninsula, northeastern Japan. Twelve samples of this fossil fauna yielded 184 species, many of which are representative upper-shelf ostracods in the modern northeastern Japan Sea. Three biofacies were defined by Q-mode cluster analysis. The two most abundant species for each biofacies are Neonesidea sp. and Schizocythere kishinouyei in biofacies N, Buntonia hanaii and Yezocythere hayashii in biofacies B, and Laperousecythere robusta and Finmarchinella daishakaensis in biofacies L. The depositional environment of the individual biofacies can be defined as (1) upper-shelf area under open-sea influence in relatively high salinity (biofacies N), (2) inner—central-bay area, with relatively low salinity (biofacies B), and (3) bay-mouth area with intermediate salinity levels between those of (1) and (2) (biofacies L). Water depth decreased from the upper-shelf area through to the bay-mouth and then to the inner-central-bay areas during the depositional period of the studied horizons. The palaeoceanographic setting during most of the depositional period was estimated as the conditions of a water mass similar to the present Japan Sea Central Water, while surface waters were influenced by currents similar to the modern Tsugaru Warm and Oyashio Cold Currents. Based on the species content of biofacies B, Buntonia and Yezocythere commonly inhabited shallow inner-bay areas around 1.2 Ma in this region, instead of the modern representative inner-bay taxa of Japan which first appeared in the northernmost Honshu region after 1.0 Ma. The occurrence mode for extant and now-extinct species of the families Hemicytheridae, Cytheruridae and Eucytheridae suggests that the ostracod fauna in the upper-shelf environment from the Hamada Formation was similar to those from the southwestern to northeastern Japan Sea coast during the same period, even though it is situated at the easternmost extremity of the Japan Sea coastline (ca. 141°E) near the Pacific.