The Echigo Plain (=Niigata Plain) located along the Japan Sea (East Sea) is one of the largest coastal plains in the Japanese Islands. The post-Würm glacial sediments are well developed, reaching a thickness over 140 m in the central part of the Echigo Plain. Diatom floral changes of the Holocene borehole cores from the Tsukigata and Shirone areas of the Echigo Plain in Niigata were examined to infer the paleoenvironmental changes in this part of East Asia. Over 290 diatom taxa were identified in the Tsukigata TG-1 and Shirone S9-4 borehole cores, and were divided into nine and 13 provisional diatom units, respectively. Most of the horizons analyzed were characterized by fresh water species, and their environments were inferred as marshes, bogs and small ponds. The major brackish water horizon dated as 10,000–6800 yr BP in the Shirone borehole core was correlated with the Jomon Transgression, which was the Holocene maximum transgression in the Japanese Islands. Several minor sea-level changes in the Echigo Plain were also recognized for the past 6800 yr, which were caused not only by global eustatic changes, but also by the relative subsidence of the basin on account of its location in a tectonically active zone.