Seventy-nine fossil ostracode species were identified in 40 of 80 samples from 15 sites of the Lower Miocene Mizunami and Iwamura Groups (ca. 18 Ma), eastern Setouchi Province, central Japan. Six ostracode associations and seven biofacies were discriminated, mainly on the basis of R-mode and Q-mode cluster analyses, respectively. Species that lived in the innermost part of enclosed brackish bay habitats became extinct and their Recent related species are absent. Most Miocene species of the genera Schizocythere, Cornucoquimba and Loxoconcha inhabited similar environments to related living species. They lived in nearshore sand and silty sand bottoms with Zostera beds under the influence of subtropical-water currents as inferred from fossil molluscan assemblages. Pseudoaurila species, which are extinct, are estimated to have been dominant on seagrass or algae during the late Early to early Middle Miocene, but after that, they were replaced by diverse Aurila and Loxoconcha species. Species of the genera Palmenella, Kotoracythere, Acanthocythereis, Robertsonites, Celtia, Elofsonella and Laperousecythere are nearly identical morphologically to cryophilic or circumpolar species living in cold water masses of northern high-latitude seas or lower sublittoral to bathyal zones in the Sea of Japan. They occur in Miocene sediments, however, in association with subtropical to mild-temperate, upper to middle sublittoral molluscan species. Ancestors of Recent cold-water species have thus inhabited Japan since at least the Early Miocene. They expanded their habitats southward according with global cooling in chron C5Dr interval (late Early Miocene) correlated with the the oxygen isotope maximum period (the base of the Zone Mi 1b; ca. 18 Ma). Eleven new species are described. This study presents the earliest Miocene record of ostracodes in and around Japan and contributes to inferences on the origin, phylogeny and speciation of Recent ostracodes living in high-latitude seas in the Northern Hemisphere.