Nankai Trough basin is an active convergent margin at south-east of Japan. Its sediments are mainly composed of sand, silt and clay together with authigenic calcite cement. Biological reactions have been realized by microorganisms and the organic materials derived to the mixture of methane and CO2. These changes occurred by bacteria and archaea under anaerobic conditions. Anaerobic oxidation of methane (AOM) have been occurred by sulfate reducing bacteria (SRB) and methane oxidizing bacteria in lower depths, which caused increasing of alkalinity in pore water leading to deposition of authigenic calcite. The existence of biofilm in thin sections indicates microbial growth in sediments. Formation of authigenic calcite is due to activity of particular bacteria such as calcinogenic bacteria, which is simultaneously accompanied with anaerobic oxidation of methane and sulfate reduction. Physiological processes and special structure of the bacteria influence on morphology and mineralogy of produced carbonate minerals.