Preliminary structural and nannofossil observations from core materials at Integrated Ocean Drilling Program (IODP) Site C0004 indicate two age reversals and a complex history of deformation in the Nankai accretionary prism. In order to improve nannofossil biostratigraphy and provide more detailed age control for understanding this deformation history, Pliocene–Pleistocene calcareous nannofossils from sediments at Site C0004 and in IODP Hole C0008A were analyzed. This study presents the nannofossil range chart for Pliocene–Pleistocene age-diagnostic species and provides a detailed record of nannofossil events and zones for three holes. The record also revealed or confirmed the presence of a number of unconformities and/or age reversals in the sediment sequence at Site C0004, providing detailed age control for constraining faulting or folding intervals.