We obtained the distribution of mean sea-level along the Japanese coast facing the open ocean for the years 1998-2007, referenced against Tokyo Peil, using Japanese Geodetic Datum 2000 (JGD2000). The mean sea-levels based on the JGD2000 were 18-36 cm higher along the Kyushu coast and 10-24 cm higher along the Shikoku coast than those from the previous datum (1969/1972). As a result, the coasts of Kyushu, Shikoku, and Honshu were divided into four sections in which the mean sea-level values for 10 years were almost even. These four sections were, in descending order of mean sea level: the coasts of the East China Sea and the Japan Sea, the Pacific coast to the west of the Cape Shionomisaki, the southern coast of Honshu to the east of the Cape Shionomisaki, and the eastern coast of Honshu. The sea-level differences at the four boundaries of each of these four sections occurred near the area of a cape attached by strong currents. The 10-year mean sea-level along the coast of Hokkaido was also higher along the Japan Sea than on its Pacific side, and this sea-level difference was concentrated near to where the current attaches the cape. The 10-year mean sea-level difference between the Honshu coast and the Hokkaido coast was 14 cm, both along the Japan Sea and within the Tsugaru Strait. Although the sea-level difference between the Honshu coast and the Hokkaido coast exhibited seasonal variation, with a peak in November, the sea-level difference between both sides of the five capes around the Tsugaru Strait exhibited different seasonal variations; this suggests seasonal variations of the current velocity in the Tsugaru Strait throughflow and the Tsugaru Warm Current near the capes. On the southern coast of Kyushu, Shikoku, and Honshu, the sea-level in the east of the Cape Shionomisaki rose due to attaching of the Kuroshio branch to another cape east of the Cape Shionomisaki at the beginning of the two large meanders of the Kuroshio, which occurred during the period of study. Following several months since sea-level in the east of the Cape Shionomisaki rose more than in non-large meander, the sea-level west of the Cape Shionomisaki lowered in the same way as the east of the Cape Shionomisaki, due to leaving of the Kuroshio branch from the cape, and became lower than that during non-large meander.