A micropaleontological study of the oldest sediments of the Cenozoic sedimentary cover of the Sea of Japan, found on the Yamato Rise, allowed us to identify the palynological assemblage of the late Paleocene age (59.2–56.0 Ma) and refine the age of the host sediments. The findings of exclusively marine microfossils (diatoms and silicoflagellates) in these sediments, the high content of geochemical indicators of paleosalinity (B, B/Ga) in them, the chemical composition of autigenic minerals, as well as the presence of organic remains close to seaweed in them, prove the marine genesis of these deposits. It is assumed that sedimentation occurred on the periphery of the epicontinental shallow sea basin under climate conditions close to subtropical.