Deep subseafloor environments are the largest carbon sink on Earth, and play a vital role in global climate control. The activity of microorganisms inhabiting these environments is a key determinant in the long-term storage of organic carbon, and yet poorly understood. Microbes performing the terminal oxidation step in organic carbon remineralization play a key ecological role, as they facilitate other carbon degradation pathways, such as fermentation, by consuming and hence preventing accumulation of their metabolic waste products to inhibitory concentrations. In this doctoral thesis, I examined patterns in the distributions of terminal carbon-oxidizing microbes that produce methane (methanogens), oxidize methane (methanotrophs), or synthesize acetate (acetogens) in the context of thermal, lithological, and geochemical gradients at three deep sea sites located on the Juan de Fuca Ridge Flank, the Peru Trench, and the Guaymas Basin. Newly-designed PCR primers made the widespread detection of marker genes possible and enabled me to construct the first detailed community profiles of methanogens, methanotrophs, and acetogens in the subseafloor. Known groups occur in addition to unknown groups and both appear zonated along sulfate concentration gradients. Stable carbon isotopic signatures of methane and acetate indicate in situ methanogenic, methanotrophic, and acetogenic activity. Possible reactions of methanogenesis, methanotrophy, and acetogenesis are discussed taking into consideration stable carbon isotopic signatures, calculated free energy yields, and substrate use by closest known relatives.