A high-resolution rock magnetic study was carried out in Integrated Ocean Drilling Program (IODP) Expedition 316 Hole C0008A located in the Megasplay Fault Zone of the Nankai Trough, SW offshore Japan, in order to document changes in magnetic properties throughout gas hydrate-bearing horizons. A total of 169 Pleistocene discrete samples were collected from~110 to 153 m core depth below sea floor (CSF), and their magnetic minerals concentration, grain size, composition, and rock magnetic parameters were estimated. Results showed the presence of iron oxides ((titano)-magnetite), iron sulfides (greigite and pyrrhotite), and their mixture, among which single-domain greigite is the most major magnetic mineral present in the samples. Two horizons containing ferrimagnetic iron sulfides (114.5-127.5 and 129.5-150 m CSF) covering almost the entire studied interval were identified, both associated with slight local pore water anomalies, suggesting occurrence of gas hydrates and anoxic conditions. These results are different from the neighboring Hole C0008C (215 m away from Hole C0008A) where four pore water anomalies and six iron sulfide-rich intervals were identified for the same time slice. Comparison of the lithology, physical properties, and geochemical data of the two boreholes at Site C0008 suggests that a combination of processes (e.g., availability of reactive iron, microbial activity) is responsible for such laterally varying distribution of the ferrimagnetic iron sulfides.