In this paper, we review research conducted during the last 20 years on the active margin that forms the Nankai Trough off the southwest coast of Japan. The Nankai Trough exists along the convergent plate boundary between the Philippine Sea and Eurasian plates. An accretionary prism and a forearc basin occur landward of the Nankai Trough. Gas hydrates have been acquired through coring in the forearc basin. Bottom simulating reflectors (BSRs), an indicator of free gas which often subtends hydrate-bearing strata, are present throughout the Nankai Trough. Slope sediments are mainly composed of fine-grained materials with low reflectivity. Instability, possibly caused by uplift or tectonic activity, occurs in the Nankai Trough with sliding being a major factor in the structuring of the terrain. Clam colonies (Calyptogena spp.) have been observed in numerous locations suggesting fluid flow along major thrust faults. When first reported, these clams represented members of the genus that had not previously been described. Most of the detailed information regarding the methane hydrates of the Nankai Trough comes from the drilling of three test wells 50 km off the Omaezaki Peninsula in water depths of 945 m. The sediments from these boreholes were dominated by calcareous, dark gray clay/silt and siltstone, with a tendency to become sandier toward the bottom of the hole. Cores collected in zones above, within, and below the hydrate-bearing strata in these boreholes show pore water chloride concentrations ranging between 100 and 550 mM with a highly variable interval occurring between 150 and 270 m below sea floor (mbsf). Compared with seawater values of 550 mM, the freshening of the porewater extracted from the cores strongly suggests the presence of gas hydrates in sediments. Pore saturation of gas hydrate estimated from the chloride anomaly was as high as 80% in sandstones in some of the sediments. Direct counts of microorganisms in the samples show cell density at 10⁵ cells/g throughout the hydrate strata, consistent with other marine sediments that have been studied. Clone libraries of the 16S, RNA gene created from extracted DNA from the Nankai Trough sediments and isolates from sediment microbial enrichments indicate the presence of methanogenic microorganisms. Sequence analysis suggests that the microbial community in the Nankai Trough sediments is distinct from those in previously characterized methane hydrate-bearing sediments on the Cascadia Margin and in the Gulf of Mexico. The majority of the sequences from the Nankai Trough clone library were either of a novel lineage or most closely related to uncultured clones. Bacterial clones exhibited sequence phylogenetic relatedness to Bacteroidetes, Planctomycetes, Actinobacteria, Proteobacteria and green nonsulfur groups, whereas the archaeal clones could be classified within the Euryarchaeota and Crenarchaeota. Continued investigations of the Nankai Trough sediments will add to our understanding of the biogeochemical characteristics of this active margin that is so important to the islands of Japan.