The substantiation of age and formation conditions of the Yamato Rise sedimentary cover, the largest rise in the Sea of Japan, is presented. Six complexes of sedimentary deposits of different age and genesis were identified based on the results of petrographic and micropaleontological analysis. Complex 1 (continental) of tuffaceous-sedimentary deposits contains numerous freshwater diatoms and palynoflora, proving the lacustrine genesis and the Early Miocene age of sediments. The age of complexes 2-6 (marine) was established on the basis of studying marine siliceous microfossils (diatoms, radiolarians, and silicoflagellates) and spore-pollen assemblages. The marine sedimentation prevailed from the end of the Early Miocene and occurred under the different conditions—from coastal-marine to bathyal. However, islands covered with forest vegetation were preserved until the Pleistocene inclusive. The irregular sedimentation during the Early Miocene and Pleistocene was associated with indented relief and active tectonics, accompanied by volcanism. The similarity of the rock complexes of the large Yamato and Krishtofovich rises (Ulleung Plateau) in age and genesis indicates the general trend of evolution of these rises, closely related to the formation of the Sea of Japan.