Microfossils abundantly occur in the upper part of the Pliocene Kuwae Formation in the Sakai stratigraphic section, Tainai City, northern Niigata Prefecture. We clarified the biostratigraphy and reconstructed the vertical paleoenvironmental changes based on micro fossils such as ostracodes, diatoms and planktonic foraminifers. As a result, the sequence in the Sakai section was divided into three parts based on lithology and correlated with the Neodenticula koizumii-N. kamtschatica diatom zone (NPD 8, 3.5-2.7 Ma). At least the lower and middle parts of the study sequence were assigned to the horizon below the datum of the rapid increase of N. koizumii (D85, 3.1-3.0 Ma). An index fossil planktonic foraminiferal species, Globorotalia inflata (s.l.), was abundantly found only in the middle to upper part of the study interval. This interval belonged to the No. 3 G. inflata bed, which has been used as a biozone in the Sea of Japan side during the Pliocene. Four ostracode bio associations were identified using R-mode cluster analysis. Based on ostracode analysis, the Kuwae Formation in the present study section was shown to have benn deposited in the sublittoral to upper bathyal zone and at least one cycle of water depth change was found. In addition, one new ostracode species, Hemicythere sakaiensis sp. nov., was described in this study.