Methane forming methane hydrates along continental margins is produced mostly by microbial methanogenesis. Results of gas compounds and stable carbon and hydrogen isotopic studies indicate that methane in these hydrates was produced by methanogens through carbonate reduction pathway. However, the geochemical interpretation is not supported by microbiological studies. From late 1980's, researches of ODP and IODP revealed that subsurface biosphere is widespread under deep marine sediments and the microbes are still active in the subsurface region. Studies of marine sediments in the Blake Ridge and the Cascadia Margin showed that numbers of subsurface microbes and their activities in the sediments were closely related with the distribution of methane hydrates in each region. Three regions are proposed as main methanogenesis location around the methane hydrate-bearing regions: (1) near surface sediments below the sulfate-methane interface (SMI), (2) sediments within the hydrate-bearing region and just below the BSR, and (3) deep region far below the BSR. So far, it is not obvious how methane provided from each region contributed to the formation of methane hydrate. Multidisciplinary studies are necessary to estimate contribution of methane provided from each region.