This study establishes for the first time in Japan a Paleogene dinoflagellate cyst biostratigraphic zonation, which enables dating and correlation of Paleogene shallow marine sediments in the northwestern Pacific where other marine planktonic microfossils are extremely rare. This study uses previously-dated outcrop sections in northern Japan and proposes nineteen dinoflagellate cyst biozones for the interval of the Paleocene-Lower Miocene, except the middle Middle Eocene where appropriate marine sections were not available. Comparison between assemblages from various other localities in Japan and Sakhalin Island, Far East Russia, confirms that the biostratigraphic zonation proposed here is applicable to the northern Japan and Sakhalin region. The taxonomic part describes 36 taxa that include three new species, Spinidinium pentagonum Kurita, sp. nov. from the Eocene, and Spinidinium? tripylum Kurita, sp. nov. and Williamsidinium diaphanes Kurita, sp. nov. from the Oligocene.