Compositions of hydrocarbon components and their carbon and hydrogen isotopic ratios suggest that natural gases from oil and gas fields in Japan are of biogenic origin, i.e., either thermogenic and / or microbial, that contribution of abiogenic hydrocarbons to the gases accumulated in volcanic rocks in the Green Tuff region is small, and that contribution of microbial methane is important even to the gases coproduced with crude oils. Diverse methanogens were detected with methanogenic activities mostly via CO₂ reduction in the brines from Minami-Kanto gas field of dissolved-in-water type, where the gases have been estimated to be microbial in origin. A large amount of methane was produced in the experiments incubating brines and sediments from Mobara in this gas field, which has revealed a high potential of in situ subsurface microorganisms to produce methane from kerogen. Methanogens, mostly classified to hydrogenotrophic type, are present in deep subseafloor sediments in the eastern Nankai Trough, and particularly abundant in those from methane hydrate concentrated zone. Anaerobic methanotrophic archaea being adapted to a low-salinity environment were also found in sediments characterized by a high percentage of methane hydrate pore saturation. In high pressure incubation experiments mimicking the oil reservoir conditions of Yabase field, a syntrophic community of acetogens and hydrogenotrophic methanogens converted acetate in the formation water to methane via a sequential reactions of acetate oxidation and CO₂ reduction. By contrast, in a high CO₂ partial pressure incubation experiments mimicking the oil reservoir conditions after CCS, acetoclastic methanogens became dominant, which converted acetate directly to methane. Methermicoccus shengliensis strain AmaM, a methanogen isolated from an oil reservoir in Amarume field was revealed to convert methoxy aromatic compounds to methane via a novel pathway including O-demethylation, CO₂ reduction, and acetyl-CoA metabolism, and also to produce methane directly from coals ranging from lignite to bituminous coal. Oils produced from Green Tuff region, including those accumulated in volcanic rocks, contain abundant >C₁₅ isoprenoid alkanes, which dictates their biogenic origin. The δ¹³C values of the oils fall in the range of those of argillaceous rocks from the same region. Maturity data such as the C₂₉ sterane 20S / (20S+20R) ratios suggested that condensates are most mature among the oils, and that the oils in the Akita Basin are generally less mature than those in the Niigata Basin. Carbon isotopic fractionations associated with the biosynthesis of hopanoids by a cyanobacterium (vs. cell) differ significantly between C₃₀ (diploptene and diplopterol) and >C₃₁ (bacteriohopanepolyols), which is consistent with the distribution of δ¹³C values among C₂₉ -C₃₅ hopanes in Miocene Monterey crude oil.