Benthic foraminifer Miliammina echigoensis diagnostic of the M. echigoensis Zone appeared in the earliest Pliocene in the Japan Sea. It was accompanied by agglutinated foraminifers including Martinottiella communis, Cribrostomoides subglobosus, Guppyella miocenica and Cyclammina japonica which had survived from the Miocene. This agglutinated foraminifer-dominant fauna flourished under the cold-water conditions in the early Pliocene. Many of the agglutinated species gradually disappeared before or in the warm/high sea-level period of the No. 3 Globorotalia inflata bed (ca. 3 Ma) and were replaced by calcareous species of the Uvigerina subperegrina Zone that bears Epistominella pacifica, Angulogerina ikebei, and Uvigerina yabei. Miliammina echigoensis and M. communis almost disappeared in the oil-field region in this period; however, they survived in the deeper part of the sea until close to the Pliocene/Pleistocene boundary at the Sites 794-797 (ODP Leg 128) and further into the Pleistocene at the Sites 798 and 799 (ODP Leg 129). The No. 3 G. inflata bed yields abundant temperate planktonic species G. inflata (s.l.) that probably migrated into the Japan Sea (embayment) through the Tsugaru Strait region, between Honshu and Hokkaido, in a warm/high sea-level period. The assemblages of the Neogloboquadirina asanoi bed, which lies above the No. 3 G. inflata bed, lack G. inflata (s.l.) and indicate a temperate-cold condition. Therefore, they are also distinguishable from the fauna of the warm Tsushima water mass. Conversely, the No. 2 G. inflata bed yields abundant Globigerinoides ruber and other warm water species, indicating the inflow of the Tsushima Current. Consequently, the initial submergence of the Tsushima Strait (Korea Strait) is inferred to have begun between the ages of the N. asanoi bed and the No. 2 G. inflata bed.