The Neogenesedimentary basins in Akita and Niigata area are typical of marine oil producing sedimentary basins in Japan. Middle Miocene source rocks of the Onnagawa Formation in the Akita oil field are characterized by a high abundance of biogenic silica. Contemporary source rocks of the Lower Teradomari and Nanatani Formations in the Niigata oil field are argillaceous with significant clay-rich clastic rocks. In order to clarify organic geochemical differences between the source rocks from these two basins, source rocks and crude oils were analyzed for biomarkers, aromatic sulfur compounds (ASC), kerogen sulfur concentrations, and oil generation kinetic parameters.Regular sterane compositions of crude oils from both basins are similar, showing major contributions from zoo- and phytoplankton. However, Akita crudes are characterized by low pristane/phytane (Pr/Ph), low diasteranes/regular steranes (Dia/Reg), low oleanane/hopane (Ole/Hop), and high benzothiophenes/dibenzothiophenes (BTs/DBTs) compared to Niigata crudes. Although the potential source rocks showed a significant variation in their organic compositions, kerogen in the Akita basin tends to have the higher atomic S/C and O/C, and lower activation energy for oil generation. Some kerogens from the central part of the Akita basin are classified as Type II-S kerogen, which are generally rich in 24-norcholestane derived possibly from diatom. Kerogens from the southern part of the Niigata basin are characterized by the lowest sulfur concentrations and the highest generation activation energies. Notably, the Onnagawa source rocks have significantly lower Dia/Reg and higher BTs/DBTs than the Teradomari and Nanatani source rocks with the same maturity levels. These organic geochemical differences between Akita and Niigata basins can be interpreted in terms of differences in oxic-anoxic condition and primary productivity at the time of deposition, the consumption of H2S by terrigenous iron at the sediment/water interface, and the abundance of clay minerals which can act as catalysts for the isomerization of regular steranes to form diasteranes during diagenesis.