Age of the Japan Sea has been controversial and its ambiguity makes an obstacle for the study of Cenozoic tectonic history of the Japanese Islands. Ages of the Japan and Yamato Basins of the Japan Sea were examined by three independent methods; stratigraphic consideration of the basin, age-depth relation, and age-heat flow relation. The stratigraphic constraints of the Yamato Basin are good by the presence of DSDP drilling holes in the central part and marginal part of the basin and bottom sampling at the outcrops of the lower sedimentary sequence. The age-depth relation of the open ocean is not applicable to the marginal seas, while the age-heat flow relation is valid in the marginal seas. Basement depths after sediment loading correction of the Japan Basin and the Yamato Basin were compared with those of other marginal basins in the Western Pacific whose ages have been well constrained. The age estimations of the Japan Basin by age-depth relation and age heat-flow relation show good coincidence. The age estimations of the Yamato Basin, however, show discrepancy among the three methods. The basement depth shows the age range of 6-0 Ma, the stratigraphic consideration shows that of around 10 Ma, and the heat flow data show estimated age older than 10 Ma. This discrepancy is due to thick accumulation of Neogene volcanonclastics (correlated to the Green Tuff Formation on Japanese Islands) which are represented by 3.5km/sec velocity layer on seismic refraction records and make an acoustic basement on seismic reflection record. As a preliminary conclusion, the age of both of the Japan Basin and the Yamato Basin is estimated to be roughly identical with the range of 30 Ma or older to 17 Ma or slightly younger. The identical age of the both basins contradicts the hypothesis of two stage of spreading of the Japan Sea; the older Japan Basin and the younger Yamato Basin. The presented age estimation is also against recently proposed clockwise rotation of the Southwest Japan at 15 Ma time with the duration less than 1 Ma which was documented by the paleomagnetic study and is believed to be a direct result of the opening of the Japan Sea. The discrepancy will be solved by a future more sophisticated understanding of tectonics of the Japan Sea.