Coenzyme F430 is the hydrocorphinoid nickel complex which acts as active site in methyl-coenzyme M reductase (MCR). The MCR-F430 complex catalyzes the last step of methanogenesis: reduction of methyl-coenzyme M to methane. Since F430 is a common enzyme for mathanogens, it can be a function-specific biomarker to estimate biomass and activities of methanogens in environmental samples. A recently developed high sensitive method for coenzyme F430 analysis and a further purification step revealed F430 concentrations at 69 and 88 meters below seafloor (mbsf) off Shimokita Peninsula (529 and 31.3 fmol g-wet(-1)) and at 60 and 275 mbsf at Nankai Trough (31.4 and 26 fmol g-wet(-1)). Estimated methanogenic biomass and activities based on reported F430 content and activities in methanogens and prokaryotic cell weight, were ranging from 3.9 +/- 10(6) to 2.7 +/- 10(6) cells g-wet(-1) and from 1.7 to 11 mu mol d(-1) g-wet(-1).