To provide insight into the biostratigraphy and evolutionary radiation of marine diatoms, Paleogene fossil records are essential because modern floral assemblages are thought to have originated in the late Oligocene. However, Paleogene diatoms are rarely reported from the Northwest Pacific Ocean because of their poor preservation and limited occurrence. In this paper, we report well-preserved diatoms from methane-seepage-induced limestone of the lower Oligocene (Rupelian) Nuibetsu Formation in the Urahoro area, eastern Hokkaido. The diatoms are dominated by Stephanopyxis spp., Odontella sawamurae, Hemiaulus spp., and resting spores. The assemblage is remarkable because it lacks late Oligocene to early Miocene index species, reflecting floral turnover during the Oligocene.