Integrated Ocean Drilling Program (IODP) Site C0002 is a key site in the Nankai Trough Seismogenic Zone Experiment for obtaining fundamental geologic information on the Kumano forearc basin and revealing tectonic activity around the Nankai Trough subduction zone. Many scientific drilling programs have been performed at this site. During Expedition 338, deep-sea cores, cuttings, and logging-while-drilling data were collected. This paper provides counting results for calcareous nannofossils in lower Pleistocene sediments from Holes C0002K and C0002L and revises nannofossil biohorizons previously recognized. Four calcareous nannofossil biohorizons in the Quaternary were detected in sediments from the two holes, and the investigated sequences can be assigned to about 1.24–1.04 Ma. Counts of subordinate calcareous nannofossil taxa were also performed to examine sea-surface environmental changes. Subtropical taxa including a Kuroshio water species were dominant throughout the section and occurred with irregular fluctuations in abundance.