Plate boundaries on the deep seafloor, such as mid-oceanic ridges and plate subduction zones, can be regarded as openings or windows through which much amount of chemical components comes up from or goes down to the earth interior chiefly by seawater convection. Recent observations with research vessels, submersibles, and drilling vessels have brought about many new findings on geochemical characteristics of hydrothermal fluid venting at mid-oceanic ridges and of cold seepage at subduction zones, both of which bear significant parts of chemical flux between the ocean and the lithosphere. This review article focuses on the behaviour of methane gas (CH4) associated with pore fluid emanation (cold seepage) from sediment of the Nankai Trough accretionary prism, which is tectonically compressed by the subduction of the Philippine Sea plate under the Japanese Islands. The origin of CH4 gas is shown to have been investigated in terms of methane/ethane ratios and carbon isotope ratios of CH4. It is also mentioned that CH4 plays an important role in producing hydrogen sulfide in surface sediment to support enormous communities of giant clams (Calyptogena) which have endosymbiotic sulfur oxidizing (chemosynthetic) bacteria in their gills.