According to many published data on the Japan Sea submarine geology of the Japanese shelf region, Paleogene and Neogene geology is reviewed in this chapter. Paleogene marine strata are recognized at south and north terminations of the Japan Sea such as off Yamaguchi and off northwestern Hokkaido, by the interpretation of seismic refraction data. The Neogene marine strata are widely recognized throughout the Japanese shelf regions of the Japan Sea. Therefore, the geological age, lithological characters, seismic profiles and fossil data of Neogene sediments are reviewed and divided into 4 parts as the off Hokkaido, the off Northeast Honshu, the off Hokuriku, San-in and kyushu, and the central part of the Japan Sea. Up to date, the oldest reliable diatom fossil zone, the Coscinodiscus yabei Zone, was recognized in the Kaiyo Seamount and the Yamato Basin.