The northern part of Honshu Island contains the major petroleum resources of Japan. The source rocks mainly comprise a sequence of Miocene marine mudstones that are overlain in places by thick Pliocene and Pleistocene sediments. In the past, mainly vitrinite reflectance analyses have been used to evaluate thermal maturities of these rocks. However, vitrinite reflectance suppression caused by compositional variation of vitrinite is common in marine-deposited rocks, and therefore, modeled estimations of the extent of petroleum generation from the Japanese sequences could be in error. Fluorescence alteration of multiple macerals (FAMM) analysis is a method that aids in solving the problem of vitrinite reflectance suppression and gives improved evaluations of thermal maturity. Combined vitrinite reflectance and FAMM analyses of potential source rock sequences intersected by the Ministry of International Trade and Industry (MITI) Shin-Takenomachi and MITI Nishi-Kubiki wells of the Niigata Basin and the MITI Honjo-Oki and MITI Yuri-Oki-Chubu wells of the Akita Basin show that vitrinite reflectance suppression is common in the Neogene source rocks. This leads to major differences between the depth profiles for vitrinite reflectance and for FAMM-derived, equivalent vitrinite reflectance. On the basis of vitrinite reflectance, the thermal maturity and hence, the petroleum source rock potential is underestimated for the Miocene Noudani Formation of the Niigata Basin and the Pliocene Funakawa and Miocene Onnakawa and Nishikurosawa formations of the Akita Basin. The new thermal maturity data indicate that these formations would have generated more oil than previously thought, such that petroleum prospectivity for areas including these sequences should be reassessed.