Stratigraphic horizons marked by the last occurrence of Spirosigmoilinella compressa and first occurrence of Miliammina echigoensis (benthic foraminifera) have been used as important biohorizons in the Neogene of the Sea of Japan region. We have elucidated the ages of these horizons on the basis of radiolarian biostratigraphy in seven onshore sections of Akita Prefecture. Age of the last occurrence of S. compressa is determined as 5.4 Ma, while that of the first occurrence of M. echigoensis as 5.2 Ma. We further reexamined the biostratigraphic ages of published data regarding cores from the deepest part of the Sea of Japan obtained by ODP Legs 127/128. The results are consistent with the ages which we obtained. Furthermore, these determined ages are close to the age of the Miocene/Pliocene boundary, 5.32 Ma. Therefore these foraminiferal biohorizons are significant in recognizing the Miocene/Pliocene boundary in the Sea of Japan region. Based on compilation of previous studies, the upper depth limit distribution of S. compressa is assumed to have been deeper than the Lower Middle Bathyal Zone, and than that of M. echigoensis from the Middle Bathyal Zone to the deepest part, which indicates their overlapping paleobathymetric ranges. Our compilation also indicates that S. compressa occurred preferably in strata deposited under a suboxic paleoenvironment, while M. echigoensis under an oxic one. Consequently, the disappearance of S. compressa and subsequent appearance of M. echigoensis suggest a change of the bottom water condition in the Sea of Japan. This paleoenvironmental change was presumably caused by the post-Messinian raised sea level in the earliest Pliocene, which enhanced the exchange of seawater between the Pacific and the Sea of Japan.