Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40 degrees C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120 degrees C hot sediments in the Nankai Trough subduction zone. Above 45 degrees C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80 degrees to 85 degrees C. In 100 degrees to 120 degrees C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45 degrees C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.