Methane (CH4) in sub-seafloor sediment is generated both biologically and non-biologically from organic and inorganic sources. A major part of the sub-seafloor methane is oxidized before leakage via “anaerobic oxidation of methane” (AOM) in the subsurface. The AOM-survivor methane, which is relatively minor part of the subsurface methane, leaches to the overlying water column and is eventually subject to thorough anaerobic and aerobic oxidation in the water column. The AOM with sulfate results in the generation of carbon dioxide and sulfide; the former (CO2) is incorporated into authigenic carbonate and autotrophic biomass, and the autotrophy is energetically driven by oxidation of the latter (H2S). These processes are typically observed at focused sites that are generally known as “methane seeps” or hydrocarbon seeps, or occasionally called as cold seeps in comparison with hydrothermal vents. Methane seeps are typically formed in passive and active continental margins, occasionally with unique features such as exposed methane hydrates, mud volcanoes, asphalt volcanoes, salt diapirs, and brine pools. Accordingly, authigenic carbonates and unique biological communities are shaped at respective methane seeps. This chapter overviews geological and biological setting for the formation of methane seeps associated with unique landscapes of carbonates and biomes.