The genus Neomonoceratina, which dominated the ostracod assemblage in the uppermost part of the Akasaki Formation (Miroku Group) of the Kyushu Island, Japan, is associated with the benthic foraminifer Ammonia cf. beccarii, mollusca Terebralia? sp. and Anomia sp., and the oogonium of Charophyceae, indicating a marine-to-brackish estuarine environment involving inflowing freshwater. This is the first record of Eocene coastal-estuarine ostracods from the eastern margin of the Eurasian continent and demonstrates that different pre-Neogene coastal-estuarine ostracod assemblages flourished in this region. The assemblages comprised five ostracod species (including one novel species) assigned to the genera Neomonoceratina, Paijeiborchella, Propontocypris and Parakrithella. These species exhibited genus-level links with the Eocene borehole cores along the continental shelf of the East China Sea and other areas of Kyushu. Fossil data of characteristic Eocene coastal-estuarine genera collected worldwide indicate that different characteristic genera inhabited each region. For example, Neomonoceratina originated on the Indian subcontinent by the Early Paleocene period at the latest, along with the northern drift of the Indian subcontinent. These species subsequently diversified west and east with the equatorial current and counter-current via the Tethys and reached the eastern margin of the Eurasian continent among the various eastwards-migrating species, where one genus ultimately adapted to the coastal-estuarine environment. Notably, the coastal-estuarine ostracod assemblage of the eastern margin of the Eurasian continent differs completely from that of the Tethys during the Eocene period. Our results suggest that coastal-estuarine ostracod assemblages are a powerful tool for palaeogeographic reconstruction.